How to make a green background as in, put the grass automatically behind it so you can use that on layer 1? Or just get rid of the background it has right now so you can use it on layer 2 over any tile?
To do the 2nd, do what RJ said; to do the first:
Open it in MS Paint (you can do it in GIMP, but this way is easier to explain)
In another window, open up any outside tileset.
Select the grass tile from the tileset and copy; make a new window and paste it in. Tile that in a 4x3 grid (the resulting window should be 128x96px).
Go back to the autotile, select all and copy.
Go to the grass window. Select "No background" (bottom left corner) and paste into place.