You can use the ebay plug with either stereo. Only those looking to change how the rest of the system sounds will benefit from using the RCA outputs.
I, for example, have split my amplifier inputs and am using 2 sets of RCA's for the factory portion of the system, while using a 3rd set for my add-in sub. I have a deck that is capable of setting different frequency cutoffs for each set of outputs so I can custom tailor how the system works.
My deck has 4.0V rca outputs and the volume is slightly less from the rca connection than it was when I had it hooked up to just the speaker outputs.