I have read most stuff posted here about making holes in a deck and rebeding hardware, including this fantastic howto by MaineSail:
Sealing Deck Penetrations to Prevent Core Rot Photo Gallery by Maine Sailing at pbase.com
My boat seems to have an extra little challenge. Inside the cabin there is a hard plastic head liner which is not laminated to the underside of the deck. Whenever a hole is drilled through the deck, it of course also goes through the head liner. So if the holes were to be taped from below then filled with epoxy, the epoxy would just run inside the headliner.
I can think of a few fixes for this, none very good.
First, I could use a very thin bolt and a very wide washer, and some kind of bridge arrangement above deck, to squeeze the headliner up against the underside of the deck. But now I have a bolt going through my epoxy I probably can not remove without damaging the epoxy.
Next, I could drill the initial hole mostly down but not completely through the deck. Say 7/8 inch if it is a 1 inch deck. Then I could use the Dremel tool to widen the hole below deck as MaineSail explains. I could now fill with epoxy and redrill the hole completely when it cures. I'm sure this is much easier said then done. Unless I get the depth exactly right the epoxy won't bond with the lower layer of deck.
Last idea, use a cork plug of some type to plug up the bottom of the hole before adding epoxy. The cork would separate when removed, but it would leave a void in the bottom part of the epoxy plug. That may not be so bad, as this is getting drilled out anyhow.
I am thinking method 3 is best, but I am hoping someone has a better idea.