Best bet is to speak to your local audio installers - whoever they may be ?? - they'll be able to advise you on any options you have.
Yes, I know they will almost probably try to push you in the direction of a new head unit, but there's no need if you don't want one.
Some amplifiers have 2 sets of inputs - my Sony unit does - one set of RCA inputs and one set for standard speaker wiring.
If you decide to stick to the standard headunit I'm sure it'll mean running a full set of cables to the amp, then all the way back to reconnect into the cars speaker wiring. Slightly over complicated I think.
If you replace the head unit, it'll mean running the RCA & switch on cabling to the amp - one way only, replacing the cars standard speakers with your replacements - using the existing wiring, and connecting any subwoofer directly to the amp.
This is what I've done. Standard door speakers replaced with Infinity & JBL units, Sony amp & 12" sub fitted in the boot.
It all depends on your budget I suppose.
* Edit * found this adaptor - http://cgi.ebay.co.uk/Boss-Audio-Hig...QQcmdZViewItem
I'm sure I have one of these lying around somewhere ....... it's yours free if you want it.