Hi Satch,
AIFF is Apple's way of storing a cd track as a file, 1:1 with no compression.
FLAC is not supported by iTunes and a pita on the Mac.
I'd go with apple lossless, too. If you already have copied lots of CDs as AIFF, just convert them (overnight maybe...) to Apple Lossless with iTunes, then throw the AIFFs away. To do that, first select the lossless encoder from preferences-advanced-importing, then create a new playlist, drop all the aiffs into it, select all the files (command-A) then right-click and choose "convert selection to apple lossless" from the pop-up menu. It will take a while, depending on how many files you've got. Make sure the macBook is attached to the power supply, too...