FLV files are very I mean, VERY compressed files and are considered more of a transport files.... converting to something else introduces another layer of degredation and you will be dissapointed with the results.
You will not make a silk purse out of a sow's ear.
Movie Edit Pro can import a huge variety of common video formats. There's also some information on that in the documentation. If you have a FLV file, it will probably be often encoded in H.264. It might be most ideal if you could find a converter that just repacks the H.264 content into an MP4 container file (without any re-encoding), which MEP could handle.