all iv ever needed to do was install mscim and mscim-tables-ja and then reboot. CTRL+SPACE switches input methods.
just hit ctrl+space and start typing in japanese and a box should pop up with the characters youre typing. press space when you want to accept what is displayed.
and yes, the scim daemon must be running, though the install and subsequent reboot should set that up for you.
check it on the command line with
$ps faux | grep scim

that said, iv had some issues recently with the kana not appearing as i type, though when i press space it appears where i was entering text. weird...