Markwi,
I usually transcode the video and resample the audio on my Linux box first, then use tmpgenc to multiplex. The simple multiplex under file->mpeg tools usually works for me. I believe the non-simple multiplex will allow you to shift the audio to line it up just right. Incidently, I have found that sox makes a much better resampled audio track than tmpgenc(at least on Best quality source, haven't tried lower). I have details on my web page at munsetrman.com

Hope that helps,
jaym