Umm yeah, I'm dubbing a Naruto episode :D (in Dutch, muahahaha). But I'm wondering, how do I voice-over the characters without screwing up the sound effects and background music?

(it's fun doing Sakura's shocked voice....)

You pretty much can't. There's a reason why so many anime's create new music and sound effects when they make a dub. The better anime dubs get the music and sound effects again for each episode from the people who originally put it together.

Whoa, so they have to assemble it from scratch everytime...? That explains why the Chinese dub of Naruto sometimes uses different background tracks XD (quite funny actually).
So I guess it's easiest to make 3 files, one with the video and the voice-overs, one with the music and one with sound FX and merge them?