I know that I'll need an auxillary input on the headunit to support the empeg.

Or, you could use the RCA outputs on the head unit going into the Empeg's Aux-in. The relative advantages and disadvantages to doing it this way have been hashed through pretty comprehensively in this thread.

My question is will a single left and right audio input sufice or will I need to find a unit w/ 2 sets of left and right inputs (front and rear)?

No, you always use only a left-and-right input. I don't think there's even a such thing as a 4-channel Aux-in.

___________
Tony Fabris