To aim the catapult, simply drag it so that it points to the target.
After it has been winched at least 10 20 laps, you can fire the catapult. Right-click the catapult, select Machine and then select 'Fire'. If it was properly aimed and winched, you will either get a message in event window that you just missed the target, or that you've hit it. If it ''only'' says that you've hit nothing, your aim is off.
<s>It is very important to remember that a catapult will only hit the fences on the north or west sides of a tile. Don't target the tile where the fences is on the south side, target the tile where the fence is on the north side. Even with very low skill you will hit most of the time or get a message saying you just missed the fence.</s>