I have no advice on upgrading, you'd have to search out products and find what you like.
As for filling In, Captain Pat's article is quite good -
http://bertram31.com/proj/tips/hole_patch.htm
Since the area is larger - I wold bevel out the glass on both sides, then construct a board and wrap it in plastic or shipping tape which resin won't stick to and then have that pressed up from the out side or the inside, does't matter which side you do first. So if you started with glassing the outside first, put the board on the inside and make sure you put protection underneath the board in case any resin were to get inside. Glass the outside, I find on my B25 hull sides, 6 layers of 1708 tends to match the hull sides thickness, so 3 layers of 1708 on the outside, Let that cure out Take the board out on the inside - layup 3 layers of 1708 on the inside.
my tip would be to cut all the glass pieces to size, label with order in which they go, and cover a table in plastic outside to wet out the glass. I personally would do 1 window at a time to not worry about working time of the resin.
Order of operation
1. wet out the edges of what is to be glassed with raw resin
2. wet out the first layer of glass (flip backside mat up first) - wet out from the bottom
3. Flip over 1st layer of glass - finish wetting out - make sure the 1st layer is flat to the layup table with no air bubbles
4. place the 2nd layer on - mat side up - wet it out
5. Flip over the 2nd layer - make sure to press it down to the first - get out any air bubbles - then finish wetting it out
6. place 3rd layer on - mat side up - wet it out
7. Flip over the 3rd layer - make sure to press it down to the first - get out any air bubbles - then finish wetting it out
Steps 1-7 should only take you @10 min for 1 of the side windows - well within normal working time for the resin - the key here is to have all 3 layers in the right orientation together as a group and wet out with no air bubbles in the mix.
8. pick up the group of layers of glass then move it over to the boat - make sure you arrange it over the hole in the right way and then press it down, work from the middle outwards with the goal of pressing the glass down and having no air bubbles, paying great attention to the area where the glass is bonding to the beveled out portion of the hull.
9. spend a few min squeegie pressing the glass down and bubble busting- the glass should be translucent and you should be able to clearly see air bubbles as a different color
10. Let it cure out overnight
11. if using epoxy - deal with amine blush -scrub surface with dish soap and scrubbing pad
12. Sand the inside to rough up the surface
13 - repeat steps 1-10 for the other side