I cut mine where you have the black line and glued that section to the boat (I would add a layer of glass on the inside next time also). At the sides and back you want to glue a piece of wood about 1/2" wide to create a flat surface for taping. this means you may want to move the cowl forward a little so you can utilize the flat section on the rear of it also.
Here is what I have been doing. Making a top to go on the top it will give you a place to put your tape and cut the cowl way down on the sides. Using the whip cowl gets a little tricky but it will work