After building many permutations of audio build outs in the TJ, the single most effective upgrade is to convert the front 5.25" coaxials into components and relocating the tweeter to the dash or a-pillar.
Adding an under seat subwoofer should be added after the fact, that upgrade is not even close to getting a decent component set up front.
You should get a 4 channel amplifier to power those and the overhead speakers in the pods.
After that I would spend money on an under seat sub.
This could be a difficult build depending on your skillset but this forum will get you through it.
Look at BLAM Relax as an superb entry level speakers. Their high end stuff costs more than our TJ and wins legit car audio contests.
No need for Crutchfield if you have this forum. Plenty of good audio guys hear to walk you through a build. DM me if you need any assistance.