Hey Straf
Congratulations on coming a very respectable joint 2nd in the Challenge
I thoroughly enjoyed reading about the dastardly plan - thank you for sharing it with us, and I also think you did splendidly with the map, considering this is your first attempt at an atlas style.
The fastest way I know of
deleting everything in a selected patch right down to the base is to make sure you have that patch selected and click on each layer then press DELETE. It erases everything in the selection area on that layer.
If you are working with layer masks and don't actually want to delete anything at all but only hide it in case you want some or all of it back at some stage, make sure the area is selected, have white picked as the foreground colour, and you have checked the 'fill selection' box on the fill tool, then go down the layer
masks one at a time, filling each with a single click of the fill bucket in the selection area.