I'm about to switch over from FCS to CS6 and was wondering if Adobe Media Encoder can utilize multiple machines like Compressor can.
I found that AE supports it, but what about Encoder or Premiere?

Additionally, I'm looking forward to the potential of working natively with AVC files - i would assume that it's no problem with just cutting; but, what about with 2 layers and tracked mattes? Would this necessitate transcodes?

Thanks for your help.

To both questions, NO.