Yes they go in the tank. There is still plently of room for the fish. Think of it as a decoration that goes in the tank, like if you were putting driftwood.
if you go to the site they tell you how much some of these stick out. for example, the "rainforest" design sticks out from the back of the tank 6" in some spots. they look pissa but seem to take up more space then I'd like. i'm still going to buy one at some point.