you have to go into "Materials" press F10 to do so. then lets say a you got a tileset you want to be transparent , go to the "Grafics/Tileset" section and click import. Next using the mouse left click on the main color outside of the tileset (aaround the tiles( and then rightclick the same spot:
the color's at the bottom should be the same color as what you don't want (what you clicked)
if that dosen't work, heck if that isnt what you needed, feel free to reply "NO" I wont mind trying again.