I would use the SPDIF out for wet, and record dry via the FX loop out.  The FX loop send is actually a 3-pin so it sends stereo, so you could have left/right wet AND left/right dry.

Place the FX Loop before the "wet" effects and set its Mix parameter to 0%.  Then it's just sending the signal, not receiving anything back into the Pod's signal.  It's basically a Y cable in your chain.  The wet effects are then processed and sent out via SPDIF.

http://foobazaar.com/podhd/toneGuide/odds#wetDry