The key to targeting a catapult is learning to target an area.

In order to target an area you need to be in mouse look mode; in the default controls either hit M to toggle it on, or hold the right click down. Also the process is much easier in third person point of view.

Once in mouse look mode, press and hold F5. A targeting indicator shoud show up underneath your feet.

Holding down F5

Moving the mouse down will move the indicator forward, and moving the mouse up will move the indicator backwards.

Still holding down F5, and moving the mouse down

Side to side motion will move the indicator side to side.

Still holding down F5, and moving the mouse down and to my left