Use this method BUT before you glue the plywood pads to the deck drill holes to suit your seat base and fit Bighead fasteners through the ply. This leaves you with a threaded bolt which you can then bolt the seat base down onto. Google for "Bighead fasteners" they are great people to deal with and they work.When I fitted a pair of pedestal seats to my boat, I cut out two circles of 3/4" marine ply then radiused the edges.
Next I mixed up a bit of fiberglass resin and coated the two circles of ply and let it dry.
I then marked where they were going to be fitted and sikaflexed them to the deck and held them in place with stainless screws. Next I got some csm (chopped strand mat) and applied a couple of layers right over the plywood circles and the whole deck. If you do this, you might want to tear the csm at the edges and overlap the next layer as cutting it will leave a visible edge, whereas tearing it will just blend in.
After fiberglassing it all, I flowcoated the whole deck. Once dry I used large stainless steel screws to hold the seats down. Never been a problem since I did that.
Hope this helps.