I don't believe the way to go is mixing epoxy super thick it needs to flow somewhat ?
But a picture of what your trying to change would allow better advise
http://i565.photobucket.com/albums/ss91/tommays/Seafever/2010_0515
_133044.jpg
On plugging just plain holes I have just beveled the carp out of the glass (12:1)and built up back to the surrounding thickness housing with various sized circles
I have also built various dams when i needed to fill and area or hold the stern tube in proper ailment until it could be reinforced with enough cloth for strength