There are a number of ways to do this. Drill all your holes in the cowl and hinge and be ready to rivet it in place. Sand the cowl in the area where the hinge is to be placed, and sand the mounting surface of the hinge with some 80 grit sandpaper. Mix up a batch of flox, which is epoxy mixed with cotton strands. DO NOT use microballons for this. Apply a thin coat of flox to the hinge and cowl, cleco the hinge in place, and then go ahead and rivet it in place while the flox is wet. Once finished, wipe off the excess flox that has squeezed out and invariably, gotten all over your tools, hands, clothes, etc. Be sure to clean the flox out of the hinge eyes and between the eyes. Once this stuff hardens, it is very difficult to sand.
Just take your time and try to be neat and it will work out fine. Also, be sure to insert your hinge pin into the hinge before setting the rivets. It will help to hold the eyes in alignment.