Hi. You can download the manual directly from the JBL support site at this link
here (it's a PDF file).
That will probably answer most of your questions, but here's a brief summary.
Q1: That's shown very well in the manual. You can use either the left or right input.
Q2:
Set the "LFE/Normal" switch to LFE. This will bypass the crossover frequency, which is exactly what you want to do if you are using the receiver to do bass management. Let us know if you aren't doing that.
Q3: The phase affects the timing of the bass frequencies relative to the other frequencies from your other speakers. Start with the setting at "0" and then adjust it to check out the effects. There is no default setting that people can tell you because it is affected by your room and set up.
Yep, that's exactly how you'd do it. It should work just fine.