I'm not sure what you mean here exactly. You say you know how to switch to Japanese input, but not how to use it when you're there?
First of all, what IME does it use? The most common one is probably scim+anthy.
Usually the shift+space combination is used to switch between modes, but others may be set up instead or as well, particularly if you have a jp keyboard. Once in jp mode, you type the romaji and hit space. This will give you a list of kanji you can select from. Then enter to move on to the next set. The F7-F10 keys are also available for selecting between various kana and romaji formats.
That's it, for the most part, though there are also many shortcuts and other commands available for use if you want them. You should find a list of them in your IME settings (though frankly I don't use most of them myself; it's too confusing to remember everything).