"Pigslo" is right to point you toward West system because it is completely reliable. However, there are a few tips maybe only learned from experience. I built a 30' catamaran in strip cedar/epoxy hulls and cabin roof, deck and cabin sides in sheathed ply. so I think you will accept I have real world experience.
Dry fit everything first before starting any coating. It is a matter of choice but I would be inclined to make the new sole removeable so you can check and replace it at any time. If you agree, then two sections will be easier - just put a strip under one side as a "land" for the other section. Get all screw holes etc in place so that no drilling is needed after coating. Bond the landing strip to one section using epoxy thickened with microfibres (not balloons or microlight). A cheap paintbrush is OK - You could wipe it off and put it into white vinegar - also good for cleaning hands & tools) but it is safer to use a new brush each time - any residual vinegar on the brush can affect the epoxy. Wear latex gloves and use paper towels to keep everything clean as you work.
For such a small area, the West System pumps are not really essential, but be careful to get the mix proportions right (5 to 1) - use a couple of old bottle lids as measures). Plastic butter containers are ideal as mixing pots. Don't mix too much at any one time. Also watch the temperature - if too cold there may be curing problems, If too hot, the epoxy may kick too soon, High humididy can also cause problems. Put four coats of epoxy onto all surfaces. Let it go off until hard, then scrub with a scourer and sandi lightly between coats (not the other way around or the sandpaper just cloggs). This removes any amine bloom and any lumps in the coating.
Rather than epoxy the sections in place, I suggest you a epoxy-bond a couple of cedar or ply bearers to the boat then use stainless or monel screws to hold the cockpit sole in place. Seal around all edges and screw heads with polyurethane sealant (Sikaflex or 3M best). Epoxy is not very UV resistant, so after installation, use a one-pack polyurethane paint.
Finally, if you decide to make the sole permanent, do exactly as above but use microfibre-thickened epoxy to create a "fillet" around all edges instead of using screws and Sikaflex
Hope this helps