On your map, every position has a ground tile (from tile A) and an overground tile (from tile B ). The overground tile defaults to the top left tile of tile B (which is also the one you should use if you want to erase an upper-layer tile). You can't see it, but it's there.
Wherever you put a tile B-E tile, the game will use the passability of that tile. But wherever you have NOT put a B-E tile, the default tile from B (top left corner) is there. That's why if you change the passage settings on that tile, you change it for almost the whole map - except those tiles where you HAVE placed a different B-E tile.
That top left tile B tile must be left blank, and have a star for passability/priority.