How to set up REL Subwoofer?

For music reproduction the high level is better, My HT is also 2 channel so I can't comment on 5.1.

For HT, you should connect an RCA (phono) cable for the .1. If you also want the sub to supplement your other speakers, then connect the REL Speakon cable to our amps speaker terminals as instructed. Both will work at the same time.

So the phono cable with .1/LFE input needs to be connected? The Neutrik Speakon cable is only a supplement? What does that mean, what does it do that the phono .1/LFE doesn't? What am I missing w/o it? Can you use the Speakon cable on it's own?

The Speakon connection routes from the speaker outputs on your amp, sending to the REL the same full-range signal that your main speakers get. The REL then applies a low-pass filter to that signal -- which you adjust on the REL for level and frequency -- and plays the lowest bass to supplement your main speakers. (Alternatively, you can send a pair of RCA interconnects to REL from a preamp output, but the Speakon is the preferred method.)

The .1 or LFE from your AV receiver is a separate channel in the mix, which contains Low Frequency Effects. While the Speakon connection is filling in the lowest octave that your main speakers may be missing, the LFE channel is supplying special effects created in the mix just for the subwoofer. You can hookup the REL with either the Speakon or the LFE, but the great thing about it is that you can hook them both up and they give you both bass supplement and LFE.

I know I haven't done the best job of explaining this. I hope it's clear.

If you think your main speakers would benefit from additional low end support from a sub then use the neutrik in conjuction with the .1/lLFE, if you feel your mains are adequate you can just use the .1/LFE by itself. The nice thing about the Rel you have is that you have separate gain controls for the LFE input and the neutrik/speakon input. You could always use the speakon connection for your center channel and use the LFE input for effects. Some people don't prefer this setup because of how the LFE track can interfer with dialogue coming from the center channel, experimentation in your system is the only way to know.