I cut the anchor well, then two coats of resin into the section that would be out of sight once the floor went in. When I was building the hull halves I built into them a couple of supports on the sides for the anchor well floor. I just used some glass tape and foam left over from the beam flanges.
The pics below pretty much show how it is.
I made sure I put in really good fillets in the corners to make sure mud does not sit in them and is easily flushed out.
The foam where the drain holes have been drilled was first removed and replaced with a glue mix (resin and microfibre).
The holes then drilled through the glue mix and outer laminate. You can just see them in the corners in this pic.