I don't run a POD - but I do take a direct guitar feed from a U5 or a GT Brick and pass it into my DAW Software for realtime amp sims in Guitar Rig and/or Amplitibe (the DAW feeds a dedicated power amp and 4x12" 1960B cabinet which is also mic'd for the speaker vibe).  This way I'm recording the clean DI signal to the DAW and can effectively change the Amp Sims during playback/mixing - or even "re-amp" using a real analog amp and mics at a later time.

I'd probably record the clean DI and the effected POD source to separate tracks - or scrap the Pod and use VST Plug-ins instead   If you want to record the POD's effected output - I'd assume the POD's digital outs would be best assuming you can get your system sync'd correctly (no clue what kind of clocking options the POD has or what other gear you need to sync in your system).  Going POD analog out to FF analog in will add a few ms of latency FWIW...