I think for the most part, your characters for original manga/comics should be located in places you're familiar with. I know I usually really hate reading western manga set in Japan with Japanese characters because you just know that the creator learned everything he knows about Japan from reading manga and anime... so, the setting isn't authentic, it's borrowed/stolen from other manga and anime.
But, a Japanese character in America (or wherever you're from) is perfectly fine, or Americans (or whatever nationality you happen to be) visiting Japan is fine. One of the X-men series a couple years ago had a cute Japanese girl in it, I remember, and she was a great character. And the X-men have also had book issues taking place in Japan. But, overall, you should stick to what you know.
the exception would be in fantasy type stories... where you can pretty much invent the world you're writing about... post-apocalyptic worlds might have all schoolgirls walking around in sailor suits and carrying katana.... but westerners drawing contemporary manga with Japanese schoolgirls in it... don't do that :-)