The Holley re-manufactured Carter I have says that all the settings should be close from the factory. If your engine is running rough, you should first check for vacuum leaks. If there aren't any leaks, adjust the idle screw until the engine idles at ~700 RPM. If the engine still runs rough or you are unable to get it to idle consistently, then you need to adjust the idle mixture. To adjust the idle mixture, there are two screws at the base of the front on the carb. These two screws need to be adjusted in or out. I recommend turning both screws all the way in and then backing them out an equal number of turns(6). Now with the engine running turn the screws in until the engine starts to get rough and then back them out one full turn. This should set the idle mixture.
I have spent a lot of time trying to get my Carter working correctly and am yet to succeed. The previous instructions are from Holley, but if you have $25 any good carb shop should be able to tune your carb and save you some headaches. I believe there are limitations to how well the Carter will work based on all of the emissions and computer controls.
Good Luck,
85 CJ7-4.2L,T-176,D300,2.5" lift,32"BFG MT,Durabak,York-Air,HEI?