There are quite a few tutorials on getting hiragana characters on Ubuntu, but many of them seem rather complicated, and very few seem to mention Karmic at the time of writing (even though it's been stable for a good few months now). I won't guarantee that this will work for everyone with Ubuntu Karmic, so please back-up important data before attempting this. Oh, and if you don't know what Karmic Koala is then you're best leaving this tutorial alone!
Now you should be ready to go! So when you're in hiragana mode, your romaji will be converted as you type, so typing "kanji" will give you "かんじ". If you want the kanji, you can press space while it's underlined to change it, and it will cycle through all possible combinations (or, in this case, to get 漢字).
If you press F7 and F6 while the text is underlined, then it will swap between katakana (F7) and hiragana (F6).
When you press return, the text will be set. Again, you can change the default behaviour, so that space or a full stop commit changes too.
Pressing Ctrl + Space a second time takes you back to the normal setting.
If you have a problem with the short-cuts, you may already have noticed that you can change them in the IBus Preferences window. I had a conflict with it using the same keyboard shortcut as auto-complete in Eclipse.