D,
There are some variations in how folks use this SMC system. I will tell you what I have evolved to and why and you can decide if this is what works well for you.
The auto level sequence designed into the system works well and activating that is what I do. It starts with an air dump, the one built into the controller is not long enough to fully drain the air springs so that alters if you end up level. Start the leveling process by holding down the air dump switch (engine off) until there is maybe 5lbs of air showing on the dash air gauge on the needle that dropped pressure. Then enable the auto level and let it do its thing, now in a calibrated way, given the air supply is depleted. I then turn my controller off (Steve's point that if you turn it off you then need to use manual retract only. The controller I think is not smart enough to know what it was doing when it was powered down). If you sense any unlevel condition later on, once leveled using the hydraulics, check the dash air needles and if the one that dropped with the air dump has risen hold down the air dump again to deplete it. This will lower the coach back onto the hydraulic jacks if air bleeding from one tank to the other has caused it to rise.
This hydraulic system is a very rigid system, being steel hydraulic jacks to the steel axles. The gentlest method of retract is to start the engine and air up the air springs. The air leveling system valves that are in a position to add air will allow air to flow and those air springs will fill and lift the coach and the hydraulic jacks off the axles (floating on air so to speak). The remainder may not where the coach is held high by the hydraulic leveling jacks. At this point I bump the manual retract button on and off, dropping the hydraulic jacks that are under tension holding the coach up, in small increments. I keep an eye on the air gauge on the dash, watching for the point where the air needle starts to drop, indicating that air is now flowing into the additional air springs. I pause until those air springs fill supporting the coach and when you have all the air suspension springs supporting the coach you can then hold down the manual retract until the all up indicator led is on.
I have the engine idling while doing the retract procedure to supply air to the leveling system. While this seems a little tedious, it is the best way I have found to make the hand off between the hydraulic system and the air leveling system without "dropping" the coach in a rough fashion using just the hydraulics only. I think this procedure makes sense but was not something that could be built into a controller given these two systems (air and hydraulic leveling) are not integrated in any way. Hope this helps.
Later Ed