It depends on the boat and the size of the Engine.
If its a small engine say a 30hp going on a small boat then probably down the centre line.
Bigger engines need to be offset to the right (or left if its a counter rotating gearbox)
But it does depend on the hull, something like a Avon searider with a 90hp on it would have an offset of anyhting between 1 and 2 inches.
Were as a 5.8m Ribcraft with a less deep V would only be offset by half an inch to three quaters of an inch.