OK here's the skinny. I just did this last week, and there are two things to note from this great link
that solved the whole problem perfectly:
1. If you use the xACT converter, you'll lose all tags and have to retag everything you convert. Not good. Not to mention that you'll still have to convert from AIFF to Apple Lossless to get the files in any compressed lossless format.
2. Xiph, used together with FLAC Importer allows you to play FLAC in the Quicktime player and other programs that support QT, but not in iTunes, unless you change the metadata of the file, which you can do with SetOggS.
If you follow the instructions on the link you'll be able to play FLAC natively in iTunes, with all tags preserved. Or you can use iTunes to convert to Apple Lossless if you like, still with all tags preserved.