Replaced 1999 xj headunit and now it's not starting, any help?
 

I replaced the stereo with a new one, I didn't disconnect the battery which was my first mistake. I used a wiring harness bought for my make and model from Walmart which made connecting the different wires simple enough. After I plugged everything in the radio works great but the next day my Jeep wouldn't start. It doesn't crank or even click when I turn the key. I hit the starter with a rubber mallet and it started however. Lights and radio still work though. I've tried disconnecting the positive and negative battery wires and resetting the theft system. But I'm lost on what to do now.

I would check to see if you have an open hot wire to the battery. Sounds to me like it was just drained. Try jumping it and see what happens.... unless you have a spare charged battery to put in for a quick test.
Check you wiring diagram again and see if you don't find a mis-matched connection somewhere. it only takes one wire staying hot to the battery to drain it.

I've gotten it to work a few times by hitting the starter , I don't know much about the electrical aspect but would the hot wire prevent the starter from working until I hit it to start it?

Pure coincidence then. Bad starter (probably oil soaked) happened to fail after stereo installation.