A couple of questions:
1. You didn't mention center channel, do you have the RC-3?
2. You list two RS-3s, was one a miss type and really the RC-3? or did you get two pairs of RS-3s, one set for surround, one set for back channel?
I have a 3801 with the following speakers:
RF-3 are 51" apart 10' front of listen post
RC-3 sets on top of TV also 10' away
RS-3 connected to Surround A, mount directly in line with my listening position 7' up on the wall.
A pair of Infinity 2000.3 connected to BACK channel mounted 8' directly behind the listening position.
If you haven't setup your system for 6.1 surround, then plan on it, remember the difference between Dolby Pro Logic and Dolby Digital? ITs the same difference!! Awesome...
I have a different subwoofer so I can't help you there.....
Hoped this helped some..