Kbarkamian, I use iTunes to sync with the iPod, but that's it. I use MediaMonkey to rip the CD's to FLAC, and I wrote a Perl program that sits on my Linux music server and runs nightly to create MP3 equivalents of the new FLAC files. This separate MP3 tree is then used for the iPod syncing. The FLAC files are used for my serving my Squeezeboxes.
I really, really wish iTunes would be able to acknowledge any new files placed in certain directories, rather than needing to add the files to the library manually. And I wish that iTunes would be able to utilize FLAC. Those are significant downsides that I see of iTunes at the moment.
Michael