Based on the way the outputs work on the riocar, will I lose with regards to how the unit does channel separation? How does this work? What exactly is the deal with the outputs on the riocar units? Is it front L/R, rear L/R? And then the headunit control features depend on this?

The outputs on the Rio Car are exactly like any other head unit. Two stereo L/R pairs, controlled by an ordinary Front/Rear fader.

If you were to use only a two channel amplifier, you would connect only one of the stereo pairs, either the front pair or the rear pair, and leave the other one disconnected. Then you would leave the Fader set to "center" at all times.