You’re right that you should be converting the Canon’s h.264 files to Pro Res for editing. The preferred way to do this is via Log & Transfer within FCP. There is a helpful tapeless workflow tutorial by Shane Ross, which should come up from a search of these boards. If you don’t have the original intact card structure, Compressor can certainly do the Pro Res transcode, but it’s not very fast. In situations like that, I tend to use MPEG Streamclip which is faster.
Compressor should do a pretty good jogb scaling the 1080 clips to 720. Go into the frames controls tab and set scaling to Best. How did you try to resize…in the Geometry tab?
Russ