My skiff manual says that this is where the fun begins. Actually, all boatbuilding is fun, isn't it? It's just that some parts are more fun than others. For instance, I really don't think I would mind if someone else offered to do all the sanding...
The backbone is on (inner stem, bottom panel, and transom). I first dryfit the 3/4in thick bottom panel around the forms and screwed it onto the midships frame, inner stem and transom with permanent silicon bronze screws. Then I unscrewed and removed it so I could spread thickened epoxy on the mating surfaces of the inner stem, midships frame, and transom, then screwed it back in place again. I added some temporary drywall screws to keep the panel on the forms.
One thing that I like about plywood is that, compared to strip building, it is really easy to get a fair curve, and you can build the hull quickly. The problem is that bending it around the forms and stem can require a great deal of force. My next kayak will definitely be plywood stitch-and-glue construction (I can't help thinking about my next boat building project already!)
After the epoxy cured I beveled the edges of the bottom panel to fit the garboard strake, the next panel from the bottom. After a lot of planing and checking the bevel for fit, the garboard was dryfit into place with permanent silicon bronze screws into the inner stem, midships frame and transom. I'll plane the garboard to size, then remove it and work on the other side before epoxying and screwing both panels permanently into place.
I counterbore or countersink the permanent screws. It's easy and requires no special drill bits -- I just make a little hole with a 3/8th inch bit and drill through the center of that with a smaller bit for a pilot hole. The screw heads will be hidden by wooden bungs (if counterbored) or thickened epoxy (if countersunk). The bungs are just slices of a 3/8th inch hardwood dowel -- nothing special. It's all going to be painted over anyway.