1st you have to disconnect the battery and pull the relays, I believe, to totally disconnect the circuit, prior to touching the wires.
My alarm system runs under my dash, done at the dealer when I bought it new. I have 4 security devices on my Jeep , and I still sleep with a firearm close by, and some silent weapons as well. My best advice is to get the factory manual , like I bought, for a hundred and some odd dollars. It tells me everything I need to know except aftermarket stuff.
Hopefully you can get at least a wiring diagram from someone here, if you let everyone know what year your Jeep is.