assuming you already have the kayak built, you might try this for positioning your doubled bulkheads.

measure along the keel line for the location where you want to put your bulkheads and make your cuts. When you have identified the spot(s) drill a 1/16 inch hole. Tap a 4d, 6d or 8d nail into this hole. you want a snug fit, and you should only drive the nail in an inch or two.

Tie one end of a string to this nail, loop the string around the boat and tie it off on the nail.

go to either sheer and pull the string so that it is as perpendicular to the keel as you can get it. Drill a hole right next to the string and put in a nail just like the first one.

go to the other sheer, and tug on the string, getting it taut. Lay a square on the deck and get the string perpendicular to the center line of the deck. You can eyeball this, too. Where the straight string crosses the second sheer, drill a hole and tap in a nail.

Now, when you look inside your kayak you'll see three alignment pins (the nails) set about 1/3 of the way around the circumference of your boat.

from the side where you have the most room to work -- probably the cockpit side -- shove some cardboard up against these pins and scribe it for making your bulkheads. Cut your doubled bulkheads together from two pieces of stacked plywood. You can secure the pieces of plywood to each other with brads. If you drive the brads at the locations where you plan to put your connecting bolts, the brad holes will serve as centers for your drill, and you won't have to fill additional little holes.

Loosely bolt your bulkheads together, leaving about 1/8th inch space between them, and insert the pair from the cockpit side. Gently push them against the nails. Then, remove one nail at a time and press the bulkhead pair forward the thickness of one piece of plywood. You should now be able to drop the nail back in its hole. It should be resting between the twow plywood pieces. Repeat this for the remaining nails.

Your nails should now all be between the two plywood parts that will become your bulkheads.

If you gently tighten the bolts on your bulkheads you will draw them snugly together, clamping the pins slightly, and automatically centering themselves.

Apply glass and resin to hold the two bulkhead parts in place. When it sets you can pull out the nails. before you do, though, sight along the string line between each pair of nails and mark a cutting line. To double check that the line is in the right place, drill a small hole on the line, about halfway between the endpoints, and probe with a wire or a brad to be sure you have hit the space between those bulkheads.

Cutting should be a snap once you get a small slot started in the exact right place. You should get some support from the fittings with the bulkheads already bolted together, so things won't fall to pieces when you get more than half the cut made.

hope this helps

PGJ