In my experience I found FS to be a hindrance more than help when it came to practical flying. At this early stage of flying, VFR in a small two seater is nothing similar to flying the heavy iron on your computer screen. I found that I was too dependent on the instruments and wasn't looking outside nearly enough as I should have been i.e. I would check the AI or the VSI or tell me if I was straight and level or what angle of bank I was rolling. It took a while to stop this and to look at the actual horizon outside the aircraft. Don't get me wrong, there are some + points. It is no doubt handy to know your 6 primary instruments and what they do. FS should also give you an insight to what makes the aircraft fly and the effects of manipulating the yoke on the control surfaces.
If you do intend to use flight sim whilst learning to fly stick to GA aircraft, I believe Flight One has a very nice model of a C150/152, and there is some good payware software available for other small aircraft also. Running through the pre-start checklists here is a good idea, as is practicing various principles which you will be required to perfect i.e. the trim wheel etc.
Vatsim is a great resource for brushing up on RT. You will learn alot of new phrases this way and will help your real-world confidence also. I know alot of people getting flustered when using the PTT button, but I think FS solved this for me anyway.
Sorry for the ramble, but to summarise; be careful about getting carried away with big planes and auto-pilots - its not required at this stage and will only serve to draw your eyes inside while on real flights.
Stick to the things you will be doing in real life, fly small planes with significant weather. Learn to operate them as close to the book as possible.
Fly online to take advantage of some of the great virtual pilots and controllers out there; a free resource is very rare is this industry.
Best of Luck!!