If you are planning to use USB, then FLAC has the worst imact on SQ of the losless formats. AIFF is not as good as .wav, but a lot better than FLAC.
I will not argue about this. Yes, FLAC is bit-perfect when data compares are done, but it compromises SQ when played back real-time. There have been a number of studies including the one in TAS that support this.
Steve N.
Empirical Audio