What is the best way to mark where the water line is on a new build? Measure from the top of the hull to the water?
If you're using a fiberglass hull, put the desired amount of weight in it and put it in a bathtub, swimming pool, etc. and see where the waterline wants to be. Mark it with a pencil/crayon/etc. Don't eat the crayon. (Joke intended for someone who probably won't see this). But yeah, things don't always work out according to the plans, it's best to see how it looks in the water.
Tape a Sharpie (or whatever) to a block measured to the draft of the boat. Keeping the boat and block flat on a table, move the Sharpie around the hull to mark the waterline.