1. the 2 channel button is for the input side, for fade control
if I had an ultra to do an install on I would have a better answer on how to utilize the factory rear speaker wires,
2. there is a quality control issue with the HK head or factory wiring, with the right front side being "phased" or wired wrong, I think most people believe the weakest link to be the head unit, since many have failed, the "fix" for head unit is to check "line voltages" very carefully AND/OR add line level converter PRIOR to operation AND to reduce the OEM VOLTAGE level from factory speaker leads with a line converter, 2 if you are running 4 channel amp.
there is not much support for diy mobile audio, if you break something the first time out, just hope it's nothing major.
your situation: YOU HAD THE RIGHT STUFF, still DO, 10ga speaker wire for power will limit expansion, but might work fine ??!, I used the BOSS 8ga kit first go around, bought it for $8 online, but the actual cable was 10ga, it kinda sounded strained, cheap assed shit, garbage really, the RF install instruction say 10ga minimum, 8ga actual true spec cable, like what you had helps the amp, you'd be better off, MAKING IT FIT
I'd run everything for a few hours with the bike plugged in
so if it fails, it fails with the fairing off
improper wiring intentional or not can cause feedback, ic failure, heat damage, potential HKU failure, etc... factory radio warranty is 12 mo.
2010 FLTRX- r o a d g l i d e