I have found that the best way to deal with FLAC and iTunes is this:

1) Take the FLAC songs and drag them into the Audio CD window in Toast
2) Make sure they're in order....if they were numbered, they're in the right order. If they were alphabetical, you need to reorder them.
3) Create a disc image
4) Mount the disc image
5) Open iTunes
6) Import however you want....it'll get the song info from CDDB

This assumes whole albums are being burned. If the album was contained in one file, you'll need to split it using xAct, but that's another story entirely.......(split by calling SHN Tool)