Assuming that you've already glued the joints assembling the deck and that it's a good 'dry' fit to the hull:

Wait until joining the two and glassing the deck before cutting the hatches out. Do the inside sheer seam work as best you can from the cockpit; Pygmy says you only need TAPE in the cockpit area anyway. If you want to tape more up to the ends, you can do that after cutting the hatches out. Lap that tape a couple of inches over the tape you did from the cockpit.

If you can, determine pretty closely where you will be putting the hatches before you join the deck and hull, then glass the underside of the deck where the hatches will be, plus a couple of inches all around. I think Pygmy says to glass the underside of the hatch anyway, and this sets things in place before any cuts are made, eliminating one possible chance for the hatch to warp re the deck. It also helps to stiffen the deck in the to-be weaker place in the deck where there will be a hole.

Another reason to wait until you've glassed the deck is to ensure the same treatment of the hatch as the deck. If you glass the deck, then the already-cut-out hatch, you run a risk that they will look different somehow because your squeegy technique varies somewhere, or you mix the epoxy different, or the glass weave orientation is a few degrees off, or... .

On my second Coho, I thought it'd be easier to install the bulkheads before joining the deck to the hull. Even though I was as careful as I could be, I think somehow I distorted the hull, so when it came time to attach the deck, they no longer matched as well as before I put in the bulkhead. If you can account for that possibility, then maybe it's still a good idea, as inside the boat is a very tight spot to work in after the deck and hull are together. Just leave, say, a 1/4" gap at the top so that it doesn't hold the deck out when you attach it.