An amp can easily be connected with an RCA thingy (sorry I don't know the technical term for it). What it does is convert your head unit speaker line outs to RCA signals for inputs. With the RCA converter thingy, the signals for the rear speakers just get used for the subwoofer (instead of the sub having it's own signal). In effect, the sub will not play as clean. I've heard several systems with this type of setup. Honestly, they aren't great but they're not horrible. The other problem with using a stock deck is that you cannot really tune the different components of your system. Most aftermarket head units have separate controls for the sub, fronts/rears, crossover, etc. With the RCA converter thingy, the signals for the rear speakers just get used for the subwoofer. In effect, the sub will not play as clean. Hope this helps/makes sense.
If you aren't too picky about quality and whatever, using the stock HU will be fine.