They should be all together on the harness, however, what I posted was for a non-bose setup. I don't own a Bose equipped Rogue so I can't check there. Outputs should only be low-level, and not speaker-level until they go to the amp.
IIRC Bass should never be coming out of one side. It's always mono, and plays the same on both channels. you can cheat and just connect the other half (white) side of the LOC to the same wires, or use a Y Splitter on the amp side to connect to Left/Right RCA input. Either way you do, your subwoofer will only play Mono Bass.
MOST mono amps have a L/R input, however output is only Mono.
Here's some pics of Mono subwoofer amps so you can see what I mean. Hook in an L/R, you're still getting Mono sound.
Kicker ZX500.1
Rockford R1200-D