Ok the sequence for this is as follows

1. Receive a leak damage chit due to receiving a broadside or such.
2. Place the chit in the Special Damage box.
3. At the beginning of each turn, before planning you put a water damage chit in a box on the ship mat damage track. You place a water damage chit on the damage track for every leak counter in the special damage box. See page 33 of rule book.

If you plan a pump water action, this will remove one water damage chit from the ship mat damage track, if not the right hand box still remove the water chit and move any other damage markers to the left to fill any gaps. Pump water will remove water damage but does not repair a leak, so beginning of next turn you will get the water damage back until the leak is repaired. The action is completed as soon as the action is revealed. See page 29 of rule book.

When you plan a repair action this is placed face up, once actions are revealed, and also counts as an action for next turn. See page 31 of rule book Repair damage
The turn following the repair action is planned you can choose what repair will take effect. If you choose to repair leak move the repair chit to special damage box. At the end of the turn remove one leak counter from the Special damage box and the repair chit goes back into your actions pool. See page 31 of rule book Repairing a leak.

Remember the repair action only repairs one leak.

If you have more than one leak then you need to repair each leak, taking water damage until all leaks repaired.

If you pm me an email I have a sequence/ player aid which may help.
Trying to get this on the files but dont seem to be able upload at moment.