he probably shouldve wiried it into the ignition switched power so that when you killed the engine, the fan stopped.
the only thing that having the fans running with NO watr flowing would do - is move air around the engine bay. maybe you could do with this if youve got two spanking hot turbos in there, but then again, youd have a turbo timer which lets the engine over-run, as well as the fan continue...
if your fan runs on when the engines stopped, you should probably take it back and ask him to instal it properly.