The auto level is just that, automatic. It has 2 ride heights NORM and ALT. ALT requires payload to lower onto the HD overloads and is used for hauling or towing heavy.
Rear wheel house liners are standard on most trims, just not all.
Setting up the WDH with auto-level is very easy and not much different than without it. My first thought that is once you adjust the ball height, if required, the settings you used on the '96 will work perfect with the auto-level as that's how it worked for both of my WDH setups.
If those settings aren't proper then you can disable the suspension and set it up like any other truck by looking at sag recovery and lowering of the front axle. Then re-enable the suspension and you're done.