Mixed formats-editing-transcoding and mastering

Hello,
My client has a project with that has mixed format and we need to figure out what workflow will be best to edit and master.
The final video will be 1-2 hours.
It will be shown primarily on the web and, at a later stage, in dvd.
There are 2 main sources:
a) screen captured video with animation codec at 1024X768, square pixel (most footage)
b) video footage shot at apparently 24p "advanced" and already digitized at 24 via Cinema Tools and converted to 29.98- non square pixel (some footage)
The client wants the final output to be either 960x720p or 800x600 h.264
Audio was recorded separately for both a) and b) so everything needs to be synced.
Project is in a FCP Studio 2 system with a G5.
Questions:
What should the sequence settings be? There isn't a 960x720 setting.
Should we uprez the DV 24p and to what?
Does the b) footage need to be converted from animation to AIC (lower data rate)? Would this be effective or introduce unwanted artifacts?
What to do with the square and non square pixel footage? Take them to AE?
Thank you for your feedback,
Mabel

well it's a 16:9 format.  Is your 640x480 material 4:3 or 16:9 widescreen, which means it's anamorphic with the display of the 640x480 image stretched horizontally?  If this material 4:3, you have to decide whether you want your sequence to be 16:9, in which case you either have black bars on the left and right of your 4:3 material or you could scale up your 4:3 material to fill the frame and lose the top and bottom part of the frame OR you can make your sequence 4:3 and "letterbox" the 16:9 material (black bars at top and bottom) or scale up the 16:9 material to fill the frame and lose the material on the left and right.  Remember scaling up will cause you to lose quality.  If you decide on a 4:3 standard def sequence, you should be able crop your 16:9 "HD" material to fill the frame and this sounds to me like the best solution.
I would use compressor to convert all your footage to a single fcp friendly format before editing.
Before you go any further,  what is your end use?  This should help decide the best way to proceed.

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