The first step is getting the map in electronic format so that you can work with it on a home computer. The second step is electronically marking up the map to highlight the trail, mark elevations, or whatever. The third step is to print the map at home, and this requires a wide-carriage color printer and the right paper. There are all sorts of high-quality papers with different degrees of waterproofness. Most of the waterproofness is not in the paper itself, but it is in the resin coating on one side of the paper. There are color laser printers, inkjet printers, and even commercial printers if you don't own one yourself. Additionally, I have rugged tear-proof papers. So, the custom map gets printed at home and carried on the trip. During the trip, if I find extra things to remember, I write them with an ordinary mechanical pencil directly onto the map. If it is something like a dot, I just mark it directly in the right place. Then, if there is additional text, I write it into the nearest blank margin of the map to explain what the dot is about.
So, the only marker necessary to carry is a mechanical pencil.
When I return home, I can add my markups to the original electronic map file.
Most of my inkjet-printed maps are waterproof enough that I can cram them into a bucket of water, leave them overnight, then dry them out and the ink has not degraded. That seems sufficient to me.