Charging problems as in what?
Your jeep has not only a computer controlled voltage regulator but also a temperature sensor.
It's located in the bottom of the battery tray, round plastic disc with a pair of wires connected to it.
This sensor tells the computer if the battery is overheating, and if so, it shuts down the alternator.
Lastly, wiring connections are a bane on jeeps. Your battery terminals need to be squeaky clean/shiny/TIGHT. Also the other ends of the cables where they terminate. All it takes is one poor connection and you'll have all kinds of problems.
Always look at the basics first when diagnosing a problem. Oh and no, you can't bypass the computer.
97 Sahara, 74 Renegade, 72 CJ5, 55 Willy's (the Beast) Boss 302, 6:34 gearing, Bose 901 speakers.
God I miss that Jeep. Forgot the kinda Jeep, 80 SX4.