Its quite simple actually, and there is a TON of info on the interwebz about it, but ill keep it simple - I am using an ECU out of a 2000 Dodge Ram 1500 base model that came with a manual transmission. This way the body harness will still connect to the ECU and the other 2 ECU plugs (engine side) will all plug in as normal. The ECU will communicate with my factory gauges as well. I didn't want to use the ZJ ECU because it was originally for an automatic, and it has a security system (the dreaded SKIM system that everyone always talks about, and causes your engine to cut fuel after a few seconds of running).
I already made the wiring harness, what I did is take the stock 4 cylinder engine harness and "blended in" what I needed to from the ZJ harness. I used the TJ harness because it would match the firewall plugs, and it was originally a manual trans jeep. If I would've used the ZJ harness I would've had all kinds of automatic trans stuff to cut out, and some other crap I didn't want to deal with. I pinned in ALL 8 injector wires into the TJ harness, that way I would have the correct lengths of wire for the injectors and wouldn't have to worry about lengths. Also a few plugs here and there were changed to match the sensors on the 5.2 engine. All relatively easy stuff, just a little time consuming. This is what makes this swap so great though, the fact that you don't need to go get some specialty ECU, or adapters, or run 2 ECUs, or anything crazy. Anyone can do it with very little knowledge on wiring. Hopefully this answered your question, but if it didn't, let me know and I will try to answer it as best as I can!