You can fill and empty without the engine running, however you can fiscally here the pumps change rpm's when you increase the engine rpm to about 1500. This makes the pumps run at optimum, making them more efficient thus reducing wear on the impellers.
Filling while still and empty while in motion will also improve your time accuracy of the system.
My fill time for the rears with 600lbs overflow bags is 8 minutes fill and 8.5 minutes empty. KGB is 6 and 6.5 respectively.