The larger alternator could potentially burn up the factory charging wire. You'll want to run a larger wire from the alternator to the battery positive, a larger wire from battery negative to the chassis, and a large wire from either the block to the chassis or the block to the battery negative. This is what we call, in the car audio world, the "Big 3." You leave all your factory wiring in place and put this in there along with it. Current always takes the path with the lowest resistance and the larger the wire, the less resistance you'll have. With a 200 amp alternator, I'd recommend doing the big 3 in 1/0 to ensure you don't melt any wiring under the hood. All the other electronics in the Jeep will be fine. They're not going to pull more current than they need.
01 TJ - 4.0L, NV3550, 2" Skyjacker budget boost, Xenon flat flares, LoD front bumper, Tuff Stuff rear bumper, RH4X4 sliders, 33" STT Pros on 15x8s