That is a very nice picture and boat. The answer to your question is no. You should never paint before applying epoxy/fiberglass. When painting wood one has to first prime...because paint actually doesn't have good "tooth", or in other words it doesn't adhere well to bare wood. Primer is formulated to stick to wood and paint will stick to primer very well. This is with standard paints of course. Some modern formulations carry their own instructions and should be followed. Paint/primer will not adhere to wood as well as epoxy. If you painted first you would be defeating part of the purposes of fiberglass/epoxy. Scratches on the bottom of a boat are normal...it's going to happen. Simple yearly maintenance is the answer. You can also use harder paints or coatings, but you are still going to get scratches. A colored epoxy may help out...but still you are going to get scratches.