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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.
Some of the most important decisions in laying out a shop involve the placement of basic machines, such as the table saw and jointer. Deciding where to put them depends in part on the scale of woodworking you do, which determines the clearance area around these machines if you need to handle long stock or large sheet goods. You’ll also want to consider work flow to avoid an excess amount of running around the shop to accomplish tasks, as well as how to power your machines without turning your shop into a snakepit of extension cords.