My bad, I neglected to mention that. I have over 30k tracks and some music I have FLAC only. I don't care what format it is on my phone but I would like to be able to sync those tracks as well.
From what I can tell, J River converts the FLAC files to ALAC (or some other format) on the fly during the syncing process, so I'll probably give that a try.
Thanks for the help