Kito;
As a former dealer who repaired thru hull holes, here is what I did depending if it is on the bottom. I would bevel the edges of the thru hull hole at a 45% angle from the inside toward the outside of the hole with the largest being on the outside. Remove any bottom paint at least two inches from the outer edges of the hole on the bottom of the hull. Sand inside 1-2 inches from the edge of the topside or inside of the hole. Clean area with acetone. Then take a piece of cardboard with two layers of glass that is a little larger than the inside of the hole of course mixed with resin and hardner. Add a little more hardner to activate it quicker and hold down over that hole so the glass will not slip. Once it starts to harden, then and only then remove you hand (wear gloves). YOu do not want the glass to sag down which is why your are holding fast. Leave it alone until completely dry. Go outside and sand that smooth. You have in essence a backing plate to work with so you can lay glass outside in the hole.
You will want to purchase a small resin roller by seacure. Cannot recall the company but begins with sea. If not, use a cheap brush. Have a small container of acetone to dip the roller in or brush. Outside, the first layer of glass should only be as big as the hole inside the hole. Resin the area and glass the first layer in and flatten out and get the air bubbles out dipping the brush in of course having been emeresed into the acetone. The next piece of glass is a little larger but you do not want to overlap the beveled areas and again flatten out and get the air bubbles out with brush or roller. After two layers, let it dry. Then sand and continue the same process until the last piece of glass is level with the hull. After drying, I use to spray a little black or gray over the outside glass repair and then sanded. If any paint was left, it showed the low areas which if too much, extra glass could be added or very little, I added a two part epoxy and sanded smooth. Then I sprayed and sanded one more time to see if the area was smooth with the hull. At that point I painted the area barrier coat.
What you have done is glassed in on a bevel edge which is much stronger vs. just straight thru edges of the hole. Also the initial sanding insured a clean prepped surface for the glass to adhere. As for the inside layer in the beginning if you want to you can sand smooth to the inside of the hull if that is what you want to do but in a sense it acts like a locking collar.
If you have any further questions, email me. I am gone Friday and Saturday to a wedding.
Starting small and attaching each edge to the existing hull seems better than attaching all pieces to just one large piece.
