I have multiple waypoint files on some of my workspaces.

Would it be possible to have a "hide all waypoints" option rather than having to deselect each file?

An alternative might be to have the program remember the last used configuration.

This is a fairly trivial change so we have snuck it into the latest maintenance release, due in a day or two. Also updating the "active" waypoint set on add/edit a waypoint, to make adding multiple waypoints to a particular set a bit less tedious.