The room correction just listens to whatever speakers you're using, and the eq applies to all the outputs, so it doesn't matter how you have stuff connected for room correction. However, the Ultra has bass management, allowing you set set a crossover for your sub, speakers, or both, and it's a really good crossover at 24dB per octave. You can also do time alignment. Why would you want to use your amp's sub output, like does it have any features? Whichever device you connect the sub to should be the device that controls the volume. If using two subs, you simply get an RCA splitter from one source to both.