You can go to the tutorials on parallax mapping, but in short most people use an invisible tileset.
Basically you make two different tilesheets for B-Tiles, one a completely transparent picture and the other a picture where the tiles are marked with arrows for the different passabilities (both regular and directional passability).
You then place your picture as the parallax of the map (you'll need a script to stop parallax movement) and use the tilesheet with the marked arrows to place whatever passability you want where.
(of course the tileset needs to be configured that each of the marked tiles has exactly the passability the arrows and marks stand for.
Then you develop the game, and just before release you change the tilesheet from the marked one to the transparent one. That way the tiles with the correct passabilities become completely transparent and the player will never see that helping sheet.