I always use the layers extension - the ability to drop dungeon dressing on the middle layer is great (this is also where I mark the dead bodies ). It does take some getting used to - mainly switching to the bottom layer to remove masking and back to the top to manipulate pc/npc tokens. But once you get things rolling it becomes 2nd nature.

Grabbing the push pin links for story pages is another bottom layer link but now I use the DM map (usually has all the same push pins) and leave it set on the bottom layer to pop up the story links.

Big thanks to Trenloe for the extension! This is one feature that makes me looking forward to FGU - for the built-in layering.