Well, if you get an amp then you definitely want to upgrade all of your speakers.... but if you like the OEM look of your factory stereo then go ahead and keep it.
You can get a line level converter to convert the speaker outputs to line level (ie. RCA Jacks) for input into any amp (~$20; may need 2, one for front and one for back):
http://www.millionbuy.com/hithlc70.html And, I'd recommend installing the line converter behind the Radio unit and running your RCA cable all the way to the Amp... that way if you upgrade your Deck later, the RCA cables are in place so your amp system is plug and play with an aftermarket Deck.
The links above all sound good and I'd also recommend aftermarket Infinity speakers as great picks.
You can research on
www.Crutchfield.com to see what fits your Jeep (and if you order from them you'll get all the necessary speaker brackets to make sure your speakers mount correctly. I'd go with 6.5" speakers all around... back in November Crutchfield had a great deal on the Polk DB series . . .
Make sure your speakers can handle the power of the Amp you choose, and that the Amp will fit where you want it.
If you're really on a budget, check out the following. I've order from both of them with no problems:
www.millionbuy.com (Great for Amplifiers)
www.hookedontronics.com