In order to be a successful researcher, you need to be aware that there are a variety of different romanization/transliteration schemes used in North America. Japanese literature specialists tend to use the modified Hepburn system found in Kenkyusha dictionaries. Japanese language teachers, if they allow romanization at all, often follow the Japanese as a Second Language format. Many students who are interested in Japanese language and culture use the word processor format. Then there is also the romanization system enforced by the Japanese government, which can throw more wrinkles into the system. North American libraries use the modified Hepburn format. Here is a pdf file of the romanization used in North American libraries.
Please read the article on romaji in Wikipedia for more information on the different systems.
You will also need to learn to cite your Japanese language sources correctly. When you are citing sources you must include both the romanized form of name/title followed by the Japanese. Please consult the Monumenta Nipponica stylesheet for help in this area.