Not sure how you have your flac files setup. I have all my studio discs ripped to FLAC using one large flac file and a cue sheet (separate, not embedded). The cue sheet info was added by EAC (from the CDDB database) when I first ripped the disc.
Using Foobar2000, the ItunesEncoder (I think the file is itunesencode.exe), and the ALAC plugin available on foobar's website, you can convert FLAC into Apple Lossless. You set up the itunesencode.exe as a custom external encoder in FLAC. Google them and you'll find exact instructions from the hydrogenaudio forums.
For me it was fairly painless - Foobar uses the cue sheet for artist, track, etc. info, and parsed out other tagging info when converting.
For me it went like this: I loaded my entire Studio folders (and sub folders) into the Foobar playlist (including only the cue sheets so it wouldn't encode the flac file as well), selected all, right-clicked and hit convert, and dumped them all into one big folder. Then I loaded the folder full of .m4a files into Itunes and everything was there - artist, album, genre, track, etc. Album Artist was missing, so for my "various artists" albums I had to edit it manually.
No flac directly. You will have to convert them to Apple Lossless.
Unfortunately I know of no way to do this and also convert the tags. If there is software that can do that (on Mac OS X), then I have not found it. Anyone?
