If you're determined to keep the factory amplifier, then your best choice is to use factory replacement speakers.
The trouble is that the factory amp has built-in crossover points and equalization that are designed to work with the factory speakers. This is a particular problem with the front door and dash speaker system. The factory 3" tweeter uses a lower crossover point than a typical after-market tweeter. The low-pass crossover point of the door speaker is designed to complement the high-pass crossover point of the tweeter so that both speakers work together to produce the full sound range. If you drop in an after-market 6x9" speaker and after-market tweeter, using the factory amp and crossovers, you'll get a "hole" in your sound because the tweeter won't play the full range that was covered by the factory 3" dash speaker. You can try using an after-market 3.5" speaker in the tweeter spot, but there's not a lot of space in the factory location.
You can bypass the factory amp and connect the factory deck's output directly to the new speakers. Unlike many OEM premium systems, the Jeep head unit's output is high-level, so it can be used to drive speakers directly without the amp. You might lose some volume, however. If you did this, you'd either want to lose the tweeters and just run a full-range 6x9" door speaker, or use a 6.5" 2-way component set and build/buy an adapter to fit the round speaker in the door opening.
Your best option would be to install an after-market 4-channel amp. If you pick one with high-level inputs (or use a 4-channel line-out converter) you could still keep the factory head unit. Then you can run a 6.5" component set in the front, and 6.5" full-range speakers in the rear, with plenty of power.
If your goal is just to replace some blown factory speakers, then I'd get some replacement factory speakers from a dealer's parts department or an online auto parts retailer.
