For Digital Video Nerds

I HATE iMOVIE. I'm working on two multimedia projects right now, and this issue with muxed MPGS is ruining EVERYTHING. Does anyone know of anything I can do? I was willing to take every single one of my clips and use FFmpeg to convert them to DV, but I couldn't get it to work. I also tried to see if my camera would record non-muxed video (which would mean having to re-shoot the whole thing), but it apparently will not.

UPDATE: Okay. Looks like I might be able to do it with MPEG Streamclip. We'll see.