Right, you need to stop the pump immediately if liquid isn't moving and the pump is running dry. This can cause permanent pump damage.
You need to open the reservoir and fill it, making sure that liquid makes it to the pump so it has something to push.
Leave the reservoir open - you need to be able to move the air in front of the liquid. As the reservoir drains, shut down the pump before it completely empties so you can fill it again. Turn the pump back on to continue filling. Let it drain the reservoir, but not empty, shut down the pump, refill.
Repeat this process over and over until the reservoir never fully empties and water/liquid begins to fill it. At that point, leave the pump on (as long as it is still moving liquid) and slowly add to the reservoir to fill it. Leave the cap off and let it run. As the reservoir level drops, add more liquid - this means you are displacing air in the loop with liquid, which is what you want.
You will reach a point where the reservoir level stays relatively the same. Cap it at this point. With the pump running, slowly rock the case and tilt it to dislodge air bubbles trapped in the radiator - they usually get trapped at the end opposite where the tubing enters, so note this while you move the case. If you hear gurgling and the reservoir level drops, it means you have dislodged an air pocket, this is good. Continue to rock and move the case for several minutes until it seems you have removed the air...there still might be some that is there, but that's fine. Fill the reservoir to mostly full, 85-90% is fine as long as the pump isn't sucking in small air bubbles. If it is, you need to look into getting something to prevent agitation in your reservoir...pumping small bubbles back into your loop means they will end up 'stuck' in your radiator and collecting.
Remember, watercooling is less effective if air bubbles exist in the radiator - it means you have less water-to-radiator thermal exchange.