MMA can't do this. You could create Auto-Playlists in MMW based on Extension and Sync those.

Hi,
You can edit collections in MM GOLD so that one exclude format. But, no MM can't treat same track in MP3 and FLAC as single library entry. Using such collections or Auto-Playlists can be used in MMA sync to separate formats.

Can MM separated files by type? FLAC in one place MP3 in another?