Green box = treasure.
Yellow box = key locked door.
Red box = spike tile.
The number in them indicates linked chests / spike tiles inside a dungeon.
Click a treasure box to mark/unmark it (like when you opened the box to help track loose items).
Double click it to mark/unmark it special (like if it was a good item you wiped on / ran from but might want to come back to later).
Double click the map itself, not one of the boxes, to horizontal flip it. This isn't perfect but should help you get a feel for it.
See also: my procgen or entrance shuffle overworld helper
