Ah, I got you! you inserted it into Free Space, so you need to change them manually. You need to do what I said before:
The box you see above the Middle Box (should have Down/Up above that) is the tile you selected, and is made of 4 Tileset tiles. Left click your new tile (Or Ctrl and drag to select more than 1, then Left Click), and left click on the small square of ground tiles, on the parts you are replacing.
Change the principal to Building tiles.