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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 o ground tiles, on the parts you are replacing.
Left click the tiles in the Left block that you want to replace (the ground tiles), and then left click your new tiles. Above the middle box, there should be a small box that appears after clicking the Left Box tiles.
Anyway, Copy and Paste your tile into the Tileset, replacing any other tiles that are old, or into blank space (it actually is more sense to recolour it then, I don't know why i said recolour it before)