Rename the WAV files to something other than WAV?

Keep two separate tree structures, one for the WAVs and one for the MP3s?

Only select and drag the MP3s onto Emplode?

Currently, there is no logic in emplode to do filtering among the files you drag onto it. If you drag a folder full of WAV files onto emplode, it's gonna synch them. Same as a folder full of MP3s or MP2s or WMAs.

I've never heard of anyone else deliberately keeping the WAVs and the MP3s together next to each other like that.

(Of course, here I am working on a set of audio mixes of some friend's music, and I'm doing exactly that-- keeping the WAVs and MP3s together in the same folder. But I'm not trying to drag the whole folder onto emplode...)