Here the airlines come into play, some have a good culture in switching AP/FD/ATHR off, some not. A good culture encourages switching AP/FD/ATHR off, and has a basic understanding among pilots and some rules when it is appropriate to do so and when not.
Once you have been accustomed to it, it is really no big deal anymore. Your scanning capacity becomes so good, that is becomes a peace of cake to supervise your autopilot.
To improve confidence of pilots who are brain washed into automation dependency, you first have to go back to basic instrument flying technique.
That means scanning the full gambit of flight instruments whether manual flying or not. The only way to do this is to turn off the flight director. The flight director is a highly compelling instrument which because of its design- keep the needles centred and everything will be fine Bloggs - means concentrating on two needles often to the detriment of correct scanning of the rest of the flight instruments. Despite what some claim it is not possible to effectively "look behind" a FD. It has to be turned off to see the full ADI picture.
One effective method to increase pilot scanning skills is to climb, cruise and descend without the distracting influence of a flight director. If you cannot fly smoothly and accurately
without using a flight director to tell you what to do, then you should not hold an instrument rating.
While there may be a regulatory side to flight director use, that would normally only apply to perhaps a take off and landing in certain weather conditions. Unless of course there is an airworthiness aspect that requires the use of an FD. For instance, can the aircraft be dispatched with an inoperative FD?
If the answer is yes, it implies the pilot should be competent to fly safely on instruments without the aid of a FD. Not every pilot is competent to do that; hence the occasional embarrassment seen in the simulator when raw data competency is supposed to be demonstrated during an instrument approach, including with a substantial crosswind.
If airlines ops management are serious about improving manual instrument flying skills - and according to the FAA they should be - then the first step is to improve basic instrument flying skills. You will never improve these skills while you are locked on brain dead to a flight director.
Once a pilot can confidently fly in VMC with the FD out of view, then flying in IMC without a FD will not hold the apprehension that seems to be prevalent in todays glass cockpits. By all means engage the autopilot and AT for complex SIDS and STARS, but switch off the FD and watch how the autopilot flies raw data. It should do it quite nicely. At the same time your own scan rate will improve greatly with exposure to all the flight instruments and not just an FD display.
Once your scan rate becomes professional, then your confidence in manual flying will slowly come back. You may even find yourself enjoying flying by hand. Try it for ten minutes or so at a time but pick the time and place to do so. If your company insists on the head in the sand approach to manual flying during line flying, at least they should heed the FAA warnings of the dangers of automation addiction and ensure each simulator recurrent training session should be equally split between automatics use and manual raw data flying.