I have a similar issue but have selected a completely different solution. I keep my entire library in Flac or MP3. I specifically chose not to go with Apple Lossless because originally it was a proprietary codec. Eventually Apple pulled its head out of its fruit and made their codec open source but alas much too late to alter my plans; by then the majority of my CD's were ripped to FLAC. I used MC to warehouse, tag and rate my music exclusively. When I want to send a playlist to my iPod or iPhone, I export the playlist to an M3U file in a shared directory on my NAS then use MediaMonkey to import the playlist. MediaMonkey will natively sync to all the Apple products and convert tracks from Flac to ALAC on the fly. There are no mirrored databases or duplicate anything, and the bonus is I never have to open iTunes