Auto level starts the sequence expecting the landing gear to have already been deployed, e.g. off the truck. When you push "Auto" the first thing to happen is the landing gear starts to retract to, I was told from the engineer (Bob T.) that this is to give the system a baseline to start leveling.
So if you just hit auto-level you may just get an error, or a sequence of events that are not desirable.
Frequently when we make a 1 night stop, campground or other, I will use the manual mode, no reason why you can't level it some with the trailer connected to the truck. If you ever watched your control pad in manual mode you will see the display will give give some relative front to back and side to side info on out of level in degrees.
If the site is fairly level I'll just use all the jacks to give some stability.
If the site is not level I will use the jacks and try leveling without lifting the truck more then an inch or so. Keep in mind that you can lift your truck if you have a short bed and not loaded up. The jacks are rated at 15,000 pounds each, but the pump is not rated that high. Still, it has a lot of lift capacity.
In my case I don't really try and lift my truck, My hitch has about 4-6" of vertical travel.