To answer the question, learn to fly your jet manually under all conditions, then and only then should you learn to let the airplane fly you...
Ideally yes. But it will never happen apart from a few minutes per hour in the simulator. Realistically most of your waking time in the simulator and the real thing will be on automatics. Manual flying scares the beejeesus out of most captains and they prefer the warm and fuzzy comfort of laid-back knob twiddling automatics. This will not change ever.