Rename the WAV files to something other than WAV?

Yes, I could do that. But I would have to remember to re-do it every time I rip another few CDs...

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

How would I configure EAC to build two parallel trees? And maintaining such a things seems like trouble.

Only select and drag the MP3s onto Emplode?

THAT is exactly what I want to do. How does one do such a thing with a folder structure?

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

Not that I am using it, but isn't that why lossless storage methods like FLAC (sp?) are around - to avoid re-ripping physical CDs when/as lossy compression technology moves forward?