I have an 2006 xA RS-3. I have the upgrade sound system which has an amp already. Is there a way I could hook up a sub/amp in the back and not mess up the current amp for my speakers? If so, How can I do it?

 

Yes, If your talking about the upgraded ipod unit. What you'll need to do is tapp the speaker wires in the dash and run it to the back. Now those are speaker level(post-amp) signals so you will need a Line Out Converter before connecting to your amp.
When its hooked up it should look like this..

Head Unit ----> LOC ----> AMP ----> SUBWOOFER.