Flushing and bleeding are two different things. Flushing is what you are talking about with no air in the system. You can do it the two man method or with a pressure bleeder.

Bleeding is when there is air in the system that you are trying to get out. In that case you need a really good pressure bleeder or do the two man method with the engine running to get the aid of the booster.

Either way, make sure you keep the reservoir full of fluid in both chambers. You have to fill enough to allow fluid to run over into the front chamber which by the way feeds the rear brakes.

Good luck,