Under the Advanced menu, there is an option to Convert Selection to AAC. This will create a duplicate of the file in AAC format. You can then create a Smart playlist that only contains AAC files and use that as the basis for further playlists or smart playlists for synching to your iPod.
Alternatively, assuming that you didn't already have AAC files that you want to keep separate from the newly created ones, sort the library by Kind and select and delete all the AAC files (e.g. to the Trash). Then shift them from the Trash to their own folder. Restart iTunes while holding down the option key to create a new iTunes Library. Import all the AAC files into the new Library.
Switch between the two Libraries by holding the option key as you launch iTunes.