Transparent (parts are clear, like the area around a character, rest is solid), or translucent (object is visible, but foggy and you can see behind it)?
Transparency works fine just by stacking tiles on top of eachother. Though you can't see parts of your characters when they walk behind transparent objects yet.
There isn't a method for tile translucency, though. So you'll have to make a new tile with the effects you want (e.g. translucently overlay an object on a tile using a graphics program, then convert the result into a tile). You can also give the illusion of translucency by making every other pixel in the tile transparent in a checkerboard pattern.
