Unfortunately, FCP isn’t really designed for editing clips like that, as you’ve found out. You’ve got a good idea to edit at maybe 15 fps instead of at 29.97 if you’re just going to compress it to a 15 fps flv file.
So you should edit at the frame rate that you’re going to deliver in and convert all the clips to that frame rate, resolution and codec to make things easier.
Are you editing in FCP5 or 6 because 6 should handle the differences better without having to render.
-Russ