Tom,
There are too many variables to answer your question. The more weight in the boat, the deeper it sinks. Then, of course, there's trim. If it's trimmed nose heavy the nose will be in deeper than the tail (bow & stern in
nauticialese) Anyway, whatever waterline you choose, your boat will never be at exactly that line for more than a second or two every other time you paddle the boat.
Best bet may simply be to select some ratio, say 25% or 40% or some other attractive number, translate that into inches of depth, and draw a straight line along one side of your boat. (Try to do it the same depth on both sides.)
Drawing that straight line can be a bit daunting. Using a chalk line is an easy method. Put a push pin in each end of the boat at your selected waterline. Get a piece of stout string about 2' longer than the boat. Tie a permanent loop (bowline knot
http://www.netknots.com/ or
http://www.realknots.com/knots/ or
http://www.animatedknots.com/index.php? ... dknots.com) into one end of the line.
Rub the line with some chalk of a color that will contrast with the background. Put the string snugly onto the two pushpins, (loop on one end, wrap the other end) pull it out and let it snap back up against the wood. It will leave a trace of chalk in a straight line. Run your masking tape along that line. Then, lightly sand off the chalk.