@tacticturtle to make something transparent, you have to adjust the alpha channel. Use the help option of the program and search for "alpha channel" in the help files. Make sure you save as a .png.
I am using Paintbrush for iMac. The only thing close to transparent is opacity, which I can't see when I draw it in with certain opaque settings on.
*Stuffs up the GUI, just for you* ;D @tacticturtle looking great so far mate. Can't wait to test the first demo of this ;3
Here is a sneak peak of the textures in-game so far. A couple are only half done, and the bedrock if you look closley, is darker. (this is in a singleplayer world)