Import your Flash-Quicktime movie into Final Cut
In the browser, right-click on the movie
Select
Make Multi-clip Sequence… from the menu
You should now have a Sequence,
Multiclip Sequence 1, that matches the settings of your movie exactly.
I usually just use H.264 when exporting from Flash. Here is a tutorial on how I export:
http://tinyurl.com/tonyteach006
keep it simple, make it perfect…