I've seen stuff about line output converters and now i've stumbled upon this thread and am wondering if I should be using the HU's RCA connections.
Yes.
In short, if you did not do any wiring outside the metra (bypassing the Bose amp) then yes, you need to be using the aftermarket hu's rca preouts.
The stock Bose system goes:
Bose hu (line level signal) ----> Bose amp, under seat (converted to speaker level) -----> Bose speakers and also a line level signal to Bose sub which is then converted to speaker level at the Bose sub amp which is located directly on the Bose sub.
So with your aftermarket hu, you are sending a speaker level signal to the Bose amp which then sends out an amp'd speaker level signal to the Bose speakers.
Easiest way to use the Rca outs is: take two pairs of Rca's, cut them both so you have about 6-8" of wire along with one side of the plugs. Strip the wires. On your harness where you connected the aftermarket hu harness to the metra, cut the 8 speaker wire connections.
The side of the speaker wires that goes to the aftermarket hu, tape up individually and tie them together so they dont do anything, touch anything.
The side of the wires that goes to the metra harness, solder/connect the stripped rca's. Keep in mind positive and negative and label them, front left, front right etc.
One the rca's connected, plug them into the correct preouts on the back of the hu, and switch the hu's output to usually an amp setting if needed.
Should be very simple.
Also to prevent confusion, each rca plug will be connected to two wires ( positive and negative)
Ex. One plug will have front left positive to one wire (usually the white or grey depending on rca) and front left negative (usually black) to the other wire.
So you will end up with 4 plugs connected to 8 wires total.