Clip resolution vs Final Cut Resolution?

I'm using an older version of Final Cut Express (came with the computer when I got it, Dual G4 867Mhz) to try to edit and add a sound track to some video captures I've made using FRAPS on my PC. Fraps natively uses a raw DV format that seems to be some obscure component video type which is incompatible with everything.
What I've done is I've taken the raw DV and run it through Virtual Dub on the PC, taking 2-5 gigs of video (approx 10 minutes worth) and slimmed it down to a very crisp 90 megs of Mpeg4 (Xvid specifically). QT and Final Cut have no problem reading this. However the capture is in 640x512, a rather awkward resolution, but it's 1/2 the native resolution of my LCD. Now I go and import these into Final Cut Express and immediately run into a problem. Final Cut only wants to work in the native resolution of a NTSC Firewire camcorder, ~700x600 or so. So what happens is the captured video is floating on a black background. Any text I add to it is added in clips that are at the native final cut resolution.
When I try to export to mpeg4 or basic quicktime this ends up looking rather odd, and rather terrible. I go from a video that is crisp and sharp in Final Cut, and in that 90meg mpeg4, and end up with something resembling colored blobs with horrifically skipping sound.
Any idea how to make Final Cut size itself to the clip being worked on and not ruin it on export?

Maurukas
FCE works in DV only for NTSC or PAL.
There's no way to change that other than bringing in the correct format in the first place.
Different formats go in about the same as the square peg in the round hole scenario.
Al

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