There is a "Trumpfactor" as John from HB says. Certain terrains will always appear on top of others, or will trump each other.
Bunker
Green
Fairway
Rough
Heavy Rough
General Terrain (desert, dirt, trees, bushes, etc.)
Bunker always overwrites green, green overwrites fairway, fairway overwrites rough, etc. So you cannot place a layer of rough over top of fairway. You just have to build two separate pieces of fairway. It's not ideal, but I think it's the only thing the game engine will allow.
When in doubt, consult the tutorial videos on the game website, or you can find the videos on youtube. The one you're looking for is Creating Surfaces: Part 1, I believe.