I was also a bit confused at how to get all the stock stuff working with an aftermarket deck, and there's a lot of bad information in this thread like using the rear speaker level inputs (already amplified) as inputs into the rear Bose sub.
First step, obviously use the base RSX (i.e. any '98+ Honda) wiring harness. Next, the wiring guide on post 2 is the key to hook everything up, so I'll just copy it:
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13
14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26
1 | GRY/RED | Passenger's Door Speaker (-), Right tweeter (-)
2 | GRN/YEL | Passenger's Door Speaker (+), Right weeter (+)
3 | BLU/RED | Constant power
4 | ------- | Not Used
5 | BRN | Radio Switch
6 | LT GRN | Rear stereo amplifier - bass signal (+)
7 | RED | Audio unit - Right Rear (-)
8 | GRN | Audio unit - Right Front (-)
9 | BLK | Audio unit - Left Rear (-)
10 | BRN | Audio unit - Left Front (-)
11 | ------- | Not Used
12 | BLU/ WHT | Left Rear Speaker (+)
13 | BLU/BLK | Left Rear Speaker (-)
14 | BLU/YEL | Right Rear Speaker (-)
15 | PNK | Right Rear Speaker (+)
16 | BLK | Ground (G502)
17 | WHT/BLU | Shielding
18 | ------- | Not Used
19 | GRN/WHT | Rear Amplifier - bass signal (-)
20 | YEL | Audio Unit - Right Rear (+)
21 | ORN | Audio unit - Right Front (+)
22 | WHT | Audio unit - Left Rear (+)
23 | BLU | Audio unit - Left Front (+)
24 | ------- | Not Used
25 | LT GRN | Left Tweeter (-) drivers door speaker (-)
26 | GRN/BLK | Driver's Door Speaker (+), Left Tweeter (+)
Instead of using 16 wire taps and making this huge mess of the wiring, I decided to solder connectors on. Soldering is really one of the easiest electrical skills, and an iron + solder cost like $6 at Wal-Mart if you just want a cheap iron to get the job done.
For the connector I used a 12" long 8 pin ATX extension cable (cost is ~$3-5). This is what it looks like:
You basically cut the extension cable in half, so you've got a male and female end. Strip the wires, then strip the wires for each of the Audio Unit inputs, and Speaker outputs. Connect 8 wires of one side of the extension cable to the Audio Unit inputs (like pin 1 of the connector is Audio Unit input LF + etc. etc.), and connect the 8 wires of the other side to the speaker outputs, obviously matching it up to what you did on the other side. This might seem complicated, but if you just print out the above wiring diagram you can make a "drawn out schematic" with which wires go to which across the connector and then wiring it all up.
Here's what it looks like all wired up:
For getting the stock Bose sub to work with an aftermarket HU, get a set of RCA cables and have them plugged into the SUB OUT on the HU. Run it down to your passenger seat area and strip the cables. The center pin of the RCA cable is positive, the outside ring is negative. Match up the two positive wires, match up the two negative wires. Then connect these to the Rear Amplifier Bass Signal wires on the stock amp harness (refer to wiring diagram above). Make sure you connect the remote wire on your HU harness (blue in color) to the "antenna" wire on the Metra harness (mine was blue/wht).
That's it, all done. Obviously don't plug in the stock Bose amp harness, but you can undo the bypass by unplugging the ATX connector.
Hope that helps clear it up some.