First I learned to do everything flying by-hand, with loads of help from this forum. Then I installed MechJeb and for a while used it as much as possible to learn its limitations and quirks. Now I understand it and use it whenever it feels good. I find I tend to use combinations of the simpler functions (MechJeb warp to apo/peri, then SmartA.S.S. to orient) and burn manually for orbital maneuvers. For ascents, I fly major changes by-hand, but when debugging or tuning a design, I love the consistency of MechJeb. In other words, I use MechJeb exactly like I'd use a real autopilot in a real airplane.
