JustinChase has it correct on the channels.
A couple other comments . . .
JRSS Subwoofer 80hz lowpass - When listening to two channel stuff, this will combine the L & R channels, add an 80 Hz lowpass, and then send it to the subwoofer output. The mains stay full range (unless bass management is used in Room Correction and Routing is set to "Move bass to subwoofer") and it doesn't do anything when the source already has content in the subwoofer channel such as 5.1 movies. If you aren't using bass management on your receiver, you might want to check out Room Correction in DSP Studio. This is more flexible and probably better quality than a receiver. If using Room Correction, you can set the Subwoofer in Output Format to Silent. However, you can still use a low pass setting in Output Format if you understand what is happening.
Subclarity - I don't use it, but it is user preference. Matt has said the following about Subclarity:
It allows quick impacts like thumps and hits to pass through, but filters out long rumbles. The goal is to remove drone from bass guitars, etc. from the subwoofer line while keeping tight hits from bass drums and other low bass.
Subclarity is one of my favorite recent improvements to the audio engine. I had always wanted something that did this, but wasn't sure it was possible. In my opinion, it works and sounds really good.
If you have a 7.1 receiver, but a 5.1 system, you can do all processing in JRiver and then copy the subwoofer to another output such as rear surround. This lets you process and use multiple subs. I can be especially helpful if the subs are different distances from the listening position.
