The number of windows, as well as their sizing and placement, depends on your orientation, view, desire for ventilation, and needs for daylight and solar gain. Orienting more of your windows towards the south side of your shop and placing them high enough that they are shaded by the eaves in summer, but allow lower-angle winter light to come in, will increase your ability to get free light and heat from the sun. If your goal is to take advantage of passive solar opportunities, make sure that you carefully research the type of glass that is in your windows and look for something with a high solar heat gain coefficient. Higher windows generally allow for benches and tools beneath them, and relatively windowless north walls may be a place to arrange wood storage or mechanicals.
One of the challenges we all face is how to move machines into a home without damaging the home, the machinery, or yourself. I actually had to bring things through the front door, and across hardwood floors, and turn 90° to descend the stairs into the shop. To protect the floors, I laid down sheets of 1/2" MDF that I could use later. On the wooden stairs, I used three strips of softwood strapping, held with wood screws to the stairs. I mounted a 2x4 baton to the wall studs at the top of the stairs, with a 5/16-inch eye-bolt through it.