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This web site
http://www.tropicalstormrisk.com
offers an e-mail alert system. Here's the alert I got this morning.

From the article:
====START QUOTE=====
Japanese officials are urging people to take the threat posed by Neoguri seriously.
"There are fears about violent winds, high waves and tides and torrential rain that we have never experienced before," Satoshi Ebihara, the Japanese weather agency's chief forecaster, told an evening news conference Monday.
"We are in an abnormal situation where serious danger is imminent," he said.
The World Meteorological Organization said Neoguri was not as powerful as Haiyan, but that "its impact is not to be underestimated".
=====END QUOTE=====
http://news.yahoo.com/japan-highest-typhoon-alert-480-000-urged-shelter-041602217.html
Japan on highest typhoon alert, 480,000 urged to take shelter
Japan braced Tuesday for one of its worst storms in years as typhoon Neoguri barrelled towards the southern Okinawa island chain, with the national weather agency issuing its highest alert and nearly half-a-million people urged to take shelter. The top-level warning means a threat to life, as well a…

The probability of getting tropical storm winds (39-73 mph or 63-118 kilometers per hour winds) in the next 36 hours is high:
http://www.tropicalstormrisk.com

If you live in an area that is susceptible to flooding or at risk from landslides, the heavy rain etc. that the storm brings may lead to a call to evacuate. I cannot promise to be able to put out such notices for people on Facebook or on the Kumamoto-i mailing list. Accordingly, if you are in a vulnerable area, I strongly recommend that you sign up for the Japanese e-mail warning messages, which you can run through Google translate as soon as you get them. Here's an explanation that I posted earlier about how to do this:
===============
Sign up for the Japanese e-mail warnings at the following address:
http://www.anshin.pref.kumamoto.jp/
If you can't read the Japanese on this page, just send it through Google translate or a similar site:
https://translate.google.com/
Then, when you get a message in Japanese from the prefecture, run it through Google translate.

The photo is from 1999 in Shiranui-machi. Homes were flooded when the combination of high tide and the swell from the cyclone caused the levees to be breached. When Typhoon No. 18 arrived that year, it coincided with oshio (大潮), a time in the month when the difference between high tide and low tide is greatest. We will be at the same time of the month when this storm hits us. The winds may not be quite as bad as was first predicted but this storm still could prove to be deadly.
http://cyber.pref.kumamoto.jp/bousai/content/asp/topics/topics_detail.asp?PageID=12&ID=18&pg=1&sort=0&PageType=list
災害記録　/　熊本県防災情報ホームページ
　平成１１年９月２３日から２４日に台風第１８号が来襲し、牛深では観測史上最高の最大瞬間風速を記録するなど、暴風が猛威をふるい、さらに、大潮で満潮時刻に近い頃に県南西部に接近したことから、不知火海沿岸を中心に高潮による被害が発生し、特に不知火町では死者１２名の大惨事となりました。この台風第１８号は、県下各地で死者１６名、負傷者３１５名の人的被害をはじめ、多数の住家に被害を及ぼし、また、農林水産業、土木施設を中心に約１,２３４億円もの被害を発生させるなど、県内に甚大な被害をもたらしました。

The probability of Kumamoto being hit by tropical storm winds in the next 48 hours is, according to this site, fairly high. The probability of having Category 1 or higher winds, however, is fairly low (you can check that out for yourself on the web site):
http://www.tropicalstormrisk.com
Still, a slow-moving storm like this one can dump a lot of water on a place in a relatively short period of time. Even if the winds don't seem too scary, the storm may still be quite dangerous.

Good news! According to this, when the typhoon hits Kumamoto, it is now predicted to be a Category 1 tropical storm -- not a Category 4 as was predicted earlier. With winds of 119-153 kilometers per hour (74-95 miles per hour), a Category 1 storm can still cause serious damage but, obviously, it's no where near as dangerous as a Category 4.
http://www.tropicalstormrisk.com

Here's the forecast for the next five days. According to this, it looks like we will begin to experience the typhoon tomorrow (Wednesday, July 9th) but that it will be closest to Kumamoto from 3 AM on the 10th (Thursday) to 3 AM on the 11th (Friday).
http://www.jma.go.jp/jp/typh/14085.html
気象庁 | 台風情報

"Evacuation of 87,000 people was announced in Kumamoto prefecture in southwestern Japan because of the risk of flooding, said Monday the NHK TV company. The evacuation of the entire population of Amakusa district, which includes the same-name city and its neighboring towns, was announced In Kumamoto Prefecture, according to RIA Novosti reports.
This was caused by the increased risk of flooding due to heavy rains. Only for one hour 70 millimeters of rain fell in the region on Monday morning. In Kumamoto, Kagoshima, Nagasaki prefecture and at Kyushu island 250 millimeters of rain fell yesterday. The Main Japanese Metrological Office warns of increased risks of floods, landslides, mountain avalanches. Kumamoto prefecture reports of landslides in residential areas."
http://voiceofrussia.com/news/2014_07_07/Evacuation-of-87-000-people-due-to-threat-of-flooding-in-Japan-media-7246/
Evacuation of 87,000 people due to threat of flooding in Japan - media
Evacuation of 87,000 people was announced in Kumamoto prefecture in southwestern Japan because of the risk of flooding, said Monday the NHK TV company. The evacuation of the entire population of Amak

"In Kyushu, parts of Nagasaki, Kumamoto and Kagoshima prefectures got more than 300 mm of rain from Sunday to Monday, prompting landslide warnings in some areas."
http://www.japantimes.co.jp/news/2014/07/07/national/typhoon-heading-toward-okinawa/
Typhoon heading toward Okinawa | The Japan Times
Typhoon Neoguri was heading northwest toward Okinawa on Monday, bringing the risk of landslides and floods to the remote island chain, the Meteorological A

Red alert for Japan’s Kyushu island as landslide loom, evacuation recommended
Japan’s Meteorological Agency has issued a red-level weather alert for the Kagoshima, Kumamoto and Nagasaki prefectures of the island of Kyushu and recommended the evacuation of about 20,000 fr

Super-typhoon Neoguri approaches Japan's Okinawa islands
Super-typhoon Neoguri, with gusts of up to 270km per hour, expected to hit southernmost subtropical island chain early Tuesday, possibly reaching mainland Japan by Wednesday

This image is from the following site:
http://www.tropicalstormrisk.com

This came from the city:
"Tropical Cyclone Information TY 1408 (NEOGURI) is comming close to Kyushu(Kumamoto)
June 11th , 2014
A heavy rain advisory has been issued for the following areas: kumamoto Pref.
Tropical Cyclone Information TY 1408 (NEOGURI) is comming close to Kyushu(Kumamoto).
Please note more Tropical Cyclone information.
Japan Meteorological Agency HP
http://www.jma.go.jp/en/typh/
If you have any concerns, feel free to contact the Kumamoto City International Foundation (Kumamoto City International Center).
(TEL) 096-359-4995 (9a.m.〜8p.m.)"
I appreciate the hard work of the city officials who put this information out in English. I think, though, that we also need an automated system in English (and other languages) that runs in parallel to the Japanese e-mail warning system.
Japan Meteorological Agency | Tropical Cyclone Information

This table is the best source I have been able to find so far for information about weather-related warnings. One problem, however, is that it doesn't say anything about the evacuation recommendations for Amakusa. It sure would be nice to have the most important information neatly packaged in one place.
http://www.jma.go.jp/en/warn/349_table.html

I won't try to explain what each of the colors and the chicken wire mesh at the top mean in detail because, frankly, the prefecture's explanation doesn't make a lot of sense to me. I can say two things, however. Red is the worst level and it means either that rivers have reached flooding level (or perhaps are already overflowing) or that there's a danger of landslides or both (both are listed as meanings in the key so this too is confusing). Places with chicken-wire mesh over the red have been told to evacuate (though the Japanese explanation does not state this clearly).
A good information science specialist needs to help the prefecture fix their system. The national government's system also has serious problems, such as putting out emergency information in pdf files that must be clicked upon. Still, one positive thing I can say about the prefecture's map is that it does give you a general idea of where the situation is the worse.
http://www.bousai.pref.kumamoto.jp/GmnDsp.exe?M100A0S0N1P0

Here's the current warning levels for Amakusa (via Google translate):
Kumamoto Prefecture
06 minutes announced 06 pm July 7, 2014
Amakusa region ● Kamiamakusa
[Continue] heavy rain, flood warning, thunderstorm advisory ● Amakusa
[Continue] heavy rain, flood warning, lightning, strong wind warning ● Reihoku-machi
[Continue] heavy rain, flood warning, lightning, strong wind warning
http://www.anshin.pref.kumamoto.jp/rireki/saigai/430031.html
Here's the information for Kumamoto City:
"● Kumamoto Kumamoto
[Continue] heavy rain warning, flood watch [warning from the alarm] thunderstorm advisory"
http://www.anshin.pref.kumamoto.jp/rireki/saigai/430000.html
The automatic translation is a bit garbled it gives you a basic idea.

Google translation of an e-mail I received:
"Amakusa Disaster Risk Management Division
I have issued an evacuation advisory to the entire city Amakusa 7 4:00 July
In addition, I established the Amakusa disaster response headquarters at the same time
In Amakusa region, and it is with heavy rain once in '50
Please have to evacuate to a safe place, such as a second floor in a house or shelter, designated as soon as possible.
Contact: Amakusa Disaster Risk Management Division Phone 0969-22-1111"
The situation in Amakusa was on NHK's national news this morning. Here's the Japanese message (for which no URL is listed):
"天草市防災危機管理課
7月7日4：00に天草市内全域に避難勧告を発令しました
また、同時刻に天草市災害対策本部を設置しました
天草地域では、50年に一度の大雨となっています
速やかに指定の避難所、または家屋内の2階などの安全な場所へ避難へしてください。
お問い合わせ先：天草市防災危機管理課　電話0969-22-1111"

Here's some more evidence about what is wrong will the prefecture's notification system. The colorful image is from the web
http://www.bousai.pref.kumamoto.jp/GmnDsp.exe?M100A0S0N1P0
and the text image is of information sent out via e-mail, though it can also be found in an archive on the web:
http://www.anshin.pref.kumamoto.jp/rireki/saigai/430000.html
The two types of information (both of which are put out by the prefecture!) use completely different terminology. The lack of a proper correspondence in the information available at the two sources is, at the very least, confusing.

Flood warnings have been issued for many areas in Kumamoto. For details, see the screenshot, which is of a Google translation of a message sent out via the prefecture's e-mail warning system.
http://www.anshin.pref.kumamoto.jp/rireki/saigai/430000.html
I've come to the conclusion that the most reliable way to get disaster information, even if you don't understand Japanese, is to sign up for the Japanese e-mail warnings at the following address:
http://www.anshin.pref.kumamoto.jp/
If you can't read the Japanese on this page, just send it through Google translate or a similar site:
https://translate.google.com
Then, when you get a message in Japanese from the prefecture, run it through Google translate. It would be nice if the prefecture could set up a system to do this automatically but, well, I wouldn't hold my breath.