To wind the clockwork engine, simply right click on it. Stop winding when the engine turns red, otherwise it will be over-wound and damage the player. It takes 4 seconds from the engine becoming red to the player taking damage.
The clockwork engine outputs between 0.5 and 1.5 RF per tick, depending on how much it is wound. As it works, it will slowly unwind, producing less energy each tick, until it is entirely unwound.