Unfortunately, neither English nor Japanese IME's on desktops provide any way to type Hepburn that isn't extremely awkward. E.g. on Windows if you want to type Tōkyō, you have to be in Hiragana mode, go letter by letter and pick from a list.
Since I'm originally from Slovakia, I used my Slovak IME, which is convenient for me.
Incidentally, Slovak has its own romanization of Japanese, which uses almost nothing but Slovak letters and diacritics (plus "w").
Wikipedia pages about 九州 and 四国:
https://sk.wikipedia.org/wiki/Kjúšu
https://sk.wikipedia.org/wiki/Šikoku
The Hepburn system is an Americanism. Americans don't own the Roman alphabet or the way it should be applied to Japanese. Though Hepburn has official status in that it is taught in Japan, and used for the benefit of visitors. E.g. signs giving names of train stations or government buildings or what have you.