Welcome to the forum, Tagg!
You just need to connect an RCA cable from the "SUBWOOFER PRE OUT" on the back of your Pioneer to the "LINE IN" on the Polk sub. I'll take a look at the sub manual in a second to see if it matters which jack (left or right) that you use on the sub.
After you get that connected:
1. Set the "LOW PASS" dial on the sub to the highest setting (160 Hz) to effectively disengage the filter in the sub because the Pioneer will take care of that
2. Rerun MCACC on the Pioneer, making sure that it detects the sub
3. After you run MCACC, you can go into the settings and check the crossovers, readjusting them if you want to
We can help you out with the crossover settings, too, if you'd like. We'd just want to know what your speakers are.