You always measure the center line of the prop with the bottom of the boat. If you have a low water pickup you can run the center of the prop higher than the bottom of the boat for speed. If you don't have a low water pickup on the lower unit, you will have to run it below the bottom of the boat. The higher you can run a outboard without losing water pressure will make you run faster.

It sounds like that everything is going to be setup for you. So just ignore everything I mentioned.