This is how I did my waterline....
I measured it from above, below and sideways to make sure it was in the right place and then lightly scored it into the glass fibre. First I marked out on the hull the exact position of the waterline at the bow and the two rear quarters. Then using these, I set the boat up square on it's stand on my flatest worktop so that the three marks were all exactly the same height above the bench. I put masking tape around the hull/stand join to keep the hull in that position. I used an engineer's combination set with a dental probe attached, which sat squarely on the bench and was able to slide around the clean worktop scribing a neat line into the hull. I then scored a second line above this to mark out the white boot-top stripe between the two. This setup can reach into the area around the hard chines forward, giving the correct width for the boot-top in that undercut.