Ive been looking to add some subs in my cargo spots just like you did. Any chance you have the blueprints or can give me some tips on the angles of the cargo spot and how you got it to fit so flush?You need to get a PAC (Line Level Input) adapter to get a audio source from the factory stereo to run your RCA's from and than to your Amp. You can tap the signal from the factory subwoofer output in the trunk, that way your factory stereo will allow you to control the subwoofer level and it will get only bass tones just like your factory sub.
As far as a setup. I have 1 10in shallow mount sub in a custom built box in my "cargo area"