If its anything like the 1200.1 then you will have two pos and two neg speaker outputs..They are on the same channel so no worries..it will basicall keep them wired in parallel, so you don't have to screw with it.
they do have terminals for two subs. if your subs are 4 ohm, then that amp will do 600+ rms combined (roughly 300 per sub). I have the same amp, along with the p80.4 for my mids/highs, and have been very pleased with both.