I love marking waypoints. I mark everything. I think it's one of the best tools to make you a more efficient and effective offshore angler is to know every little detail about an area and to know exactly where everything is.
The problem is saving all those different waypoints bogs down the performance of your fish finders/chart plotters.
I have my own system to manage my waypoints that I think works really well. It involves creating a waypoint file for each lake that you visit, stored on a memory card and deleting all waypoints off your unit except the current lake that you're on. Check out the video below to see how I do it.