>> would it be better to wait until epoxy has cured and the sand the deck to remove the bubbles  

Unless you want bubbles in your permanent finish, yes.

>>what would cause this?

Several things. Mixing the epoxy too vigorously and stirring in air bubbles. Applying with a roller. Outgassing. That is, air trapped inside the wood pores escaping as the epoxy cures. Working the glass cloth too much while wetting it out.

The good news is that if it was one of the last two, you don't have to worry about a repeat unless you're putting down new glass.

>>I don't want to apply too much epoxy.

The fix for this and preventing bubbles (and drips) in fill coats is the same - apply a thin layer of epoxy with a foam roller and tip it out. That is, lightly pass the tip of a dry brush over the new epoxy to pop the bubbles. I like a disposable foam brush for this. Coats applied this way are so thin that they never sag or drip and the tipping eliminates bubbles. Because they're so thin, you'll need to apply more coats. I typically find that I need 5 - 7 coats instead of 3.

Also, since the weave is already filled in some spots, don't put epoxy there. Save it for the low spots, only.

Good kuck,

Laszlo

   Thanks for all the tips Laszlo

Lazlo

I like the idea of using a foam Roller to apply thin coats of Epoxy and prevent runs. Is there a particular roller you use for this? Low pile, I would assume? Do you actually use the roller for the first coat over the cloth? Do you still pour the epoxy onto the hull or deck , and then spread the epoxy with the roller.