It's a long, busy list of waypoints, but I keep most of them disabled except when I'm planning new shafts.
I switched to using a spreadsheet grid to keep track of where I've looked and what I've found. I suppose a minimap mod that allows grouping waypoints so they can be enabled/disabled together (not just by dimension) would work too. I don't see a way to do that in JourneyMap. I haven't used Xaero's, so for all I know, it might have something like that.