Insert the tip of a utility knife into the edge of the window frame where it connects to the sash, and run it all the way around to break the seal. Use a putty knife to pry away the stops from the sash, and pull out the brads with needle-nose pliers. Grasp the sash and gently pull it out of the window.
Loosen and remove the screws in the frame surrounding the glass. Avoid removing all the screws; remove only those on opposite sides so it is easy to reassemble.
Pull the glass away from the window frame carefully. Gently tap the frame to loosen the glass so it is easier to remove. However, avoid damaging the frame by pounding it hard. Pull out the rubber gasket surrounding the glass.
Lay the two replacement glass panels over each other, with the aluminum spacer that comes with the frame in between. Place the rubber gasket over the edge of the window and carefully press it in place, working from one end to the other. Wear thick rubber gloves to prevent cutting your fingers when working around the edges of the glass.
Set the window panels back inside the frame. Once it's installed, tighten the screws at the corners you had loosened when removing the damaged windows.
Insert a cartridge of silicone caulk into a caulk gun. Cut a tiny opening through the caulk cartridge’s nozzle with a sharp knife. Ensure that the hole is slightly smaller than the width of caulk needed to fill the gaps.
Apply a thin bead of silicone caulk to gaps between the window frame and gasket to seal any outlet for moisture. Press the caulk into the gaps with a wet thumb and leave the caulk to cure for the time specified on the label’s directions.