OK, I went through the configuration again and made sure I set the speakers to small and the subs were set to on. Everything looked great. I then ran the MCACC again, using the manual to step me through it. They still didn't work. Then, I plugged the RCA Y cable into both the subwoofer 1 and subwoofer 2 ports on the receiver and then out to the amplifier. Both of the subs are now producing a little bit of sound, BUT, there is a noticeable hum coming from them at all times.
The bad news is that the store I bought the speakers from is in Idaho and I am in Maryland. The guys that came out to set up my projector, screen and speakers are a local A/V company. I think what I need to do is try to find a local Klipsch/Pioneer installation company and have them take a look. Before I do that, I am going to take the other advice and call Pioneer to have them step me through the connections to make sure they don't see anything first.