Measure the gross opening of your window, including both the window and the window frame, with a tape measure.
Leave the protective paper layer on the sheet. Use a circular saw with a carbide fine-tooth panel blade to cut the polycarbonate sheet to the same size as the gross window opening.
Mark drill holes around the perimeter of the sheet, a minimum of 1 1/2 inches from the edge. For normal applications, put drill marks at all four corners of the sheet, and space additional drill marks about 24 inches apart. For installation in hurricane areas, space drill marks 6 inches apart.
Use an electric drill and a carbide 1/8-inch pilot bit to drill 1/8-inch pilot holes through the drill marks. Drill your final drill holes. For normal applications you will use a #10 wood screw long enough to go about 3/4 of the way through the window frame. This screw normally requires a 13/64-inch hole through wood, but for polycarbonates, use a slightly larger 1/4-inch drill bit to allow for polycarbonate expansion. In hurricane areas, use a #14 screw, which, for polycarbonates, requires a 9/32-inch drill bit.
Place the panel over the window and frame. Use an ordinary #2 pencil, sharpened but not to a point, and mark through the panel onto the window. Remove the panel. Use your 1/8-inch pilot bit to drill into each of your drill marks about halfway through the frame. Use an appropriate drill bit for your final drill holes. If you used the 1/4-inch drill bit for for the polycarbonate, drill into the frame with a 9/64-inch or 5/32-inch bit, depending on the hardness of the frame. If you used a 9/32-inch bit for the polycarbonate in hurricane areas, drill into the frame with a 5/32-inch or 11/64-inch bit.
Insert a Phillips head bit in your electric drill. If the drill has more than one speed, select the lowest speed. Pull the protective paper about 3 inches away from the edge of the polycarbonate panel, but don't remove the sheet. Using your drill and Phillips-head screws of appropriate dimensions, attach the panel to the window frame. Pull away the protective paper sheet.