I have the drain line plumbed into the pump (along with the lower drain line from the sand & gravel filter) I push one valve closed to shut down the incoming "clean" water, and push another valve closed that goes to the sand & gravel filter. Then I open the drain valve from both the sediment chamber and the sand and gravel filter, and open the valve that goes out to the yard drain. The pump then becomes the waste pump.
Many of Kent's ponds use a separate waste pump, I think the brand he uses most is Tsunami. I had thought about going this route if my design of using the same pump did not work, but the system works just as it should. To be honest, the process is as easy as can be, and only takes a few minutes to preform.