youi can leave the factory equipment in there. now you will need to do a couple things.
1) you will need a line level converter to change speaker wire over to rca's to feed the sound signal to your amp. part is normaly about $30+ for a good one.
2) make sure when you use that line level converter you connect it to either a sub/full range signal. and also it's in phase (as in r+ is connected to r+ etc etc). if you hook that up to a tweeter, for instance, your sub won't do anything since the signal is alrdy crossed over to not play any bass.
with that said a new head unit would be a much cleaner sound signal and in alot of cases give you nice features like sub control and i-pod/usb hook ups, which are great if you plan to go off-road
another thing when you tune the system start w/ your factory stuff 1st. set bass @ 0 (in some cases lower) then see what volume you can turn it to w/o any distortion, then adjust the sub to that point. that way you can make sure @ that volume you'll be fine. biggest issue ppl have is not hearing the distortion once bass is added bc it will mask the factory stuff and w/ road noise and top off will make it worse. thats why speakers blow up so easily.
in my 95 wrongler i have a full system, 6 mid's & highs and a single 12" sub. i have had it for over 6y and never blew a thing up bc i know the limit of the system and don't go above it even it i feel the need to
hope this helps some .. feel free to ank any other questions, i work in stereo industry