Align the mortised end of the flush bolt router jig with the door's bottom edge. Twist the jig's clamps clockwise to secure the jig to the door. Select a router bit according to the flush bolt manufacturer's specifications; the bit must route to the precise depth and width of the flush bolt.
Mount the bit to the router and adjust the bit's depth to the deep mortise dimensions specified by the flush bolt's manufacturer. Rest the router's plate on the jig's edge and align the bit with the channel that cuts through the door's stile. Move the bit away from the door.
Activate the router and slide the spinning bit through the jig's channel until the router halts against the jig's stop plate. Remove the router from the jig and allow the bit to stop spinning. Rotate the router and align the bit with the channel that cuts through the door's bottom rail.
Activate the router and slide the bit through the channel until the router halts at the jig's stop. Remove the router from the jig and allow the bit to stop spinning. Remove the stile-side stop plate from the jig. Reduce the router bit's depth of cut to the shallow mortise dimensions specified by the flush bolt's manufacturer
Align the bit with the stile channel. Activate the router and push the router until it halts against the end of the channel. Remove the router from the jig. Turn the jig's clamps counterclockwise to loosen.
Remove the jig from the door. Fit the flush bolt into the mortises, long side on the stile and short side on the bottom rail. Use a screwdriver to drive screws through the flush bolt's screw holes and into the door.