Yes, the protein skimmer will add to the amount of flow in your tank if you have a hang-on-the-back.
The flow in your tank, 12.2, is not bad, but it is not the greatest either. As long as you have good water movement and good currents, I would not worry about increasing the flow at this point in time.
You can turn the filter on whenever you are done adding the salt into your tank and mixing it.