My workflow is Logic Express 8 (mixing) > Wave Editor (tracking/resample/dither).
Express is awesome for mixing, but does not have the ability to track. I used to use SoundStudio for tracking, but there was a crazy good deal on Wave Editor a while back so I jumped on that. It uses the iZotope resample & dither algorithms which I believe are shown to be better than the Logic math. It can also export directly to Flac.
Logic Studio includes WaveBurner which would replace Wave Editor. Not sure if it will allow you to export > FLAC. Logic studio is also bundled with a bunch of other apps, that if you are not creating music, you will not need.
-jay