Well.....the right way/short answer....you can't.
If you want to just "rig" a subwoofer in than yes just tie into the rca's you are using now.
The reason I say "can't" is your iPod doesn't have a dedicated sub out like a regular car radio. Subwoffers are suppose to only have to handle the low tones...thus the name "sub". If you just tie them in than they will be treated just like any other speaker and I don't think you will be happy at all with their performance.
IF you want to get a little more in depth with the sound system, than what you need to get is a cross over.....try to get one that has hi's, mid's, and low's....then you will want to hook the subs up to the low's....then you want some nice midrange speakers to hook to the mid's and some tweeters to hook to the hi's. To pull this off you will need amps to handle the 6 channels you will want. Of course all this is handled within a nice "standard" radio.....