I did contact tech support about this issue, and here's the exchange:

PG Music: The Audiophile is programmed to automatically use the WAV files. There is no setting inside the program to change this, so you won't need to worry about using the WMA files instead. The only time the WMA files would be used instead is if the WAV files aren't present. This would happen if you installed the full program on your computer's internal drive, since that option only installs the WMA files. If you use the Audiophile straight from the external drive then it will use the WAV files.

Me: Thank you, but what about a third possibility? I installed the full program to my computer's internal drive, and then copied the RealTracks and RealDrums to an external USB drive. In the programs I specified the paths to these folders. But they contain both .wavs and .wmas.

It sounds like you are saying that the program will always use the .wavs in this case, assuming they are present...correct?

PG Music: That's correct, if the Audiophile sees that both WMA and WAV files are present for a RealTrack then it will always use the WAV files.