you can do this very pretty with sgdk.
in the graphics editor, and then in the cell manager window, click with your mouse on one tile and hold the button down when you move the mouse around. so you can select f.e. three tiles in a row, or 2x2 tiles or more.
now you can paint seamlessly.
also note the very usefull functions in the toolbar "offset and wrap". wrap one tile and paint in the middle, wrap it one more time and you have the original tile, but the left and right border will have no seam.