You should have it run 24/7, nonstop (unless you are cleaning the tank or doing water changes).
That's pretty much it... overflow box brings water down, pump brings water back up. Just make sure that the pump can't pump as fast as the overflow is rated for. Otherwise, you would end up with an empty rubbermaid container, an overflowing main tank, and a burnt pump. 8O If you put a valve on the return line, just make sure that it's on the exit end of the pump, not the intake.
One thing that I will ask others... how would you put baffles in a rubbermaid?
Not sure if plexi glue would bond the rubbermaid to plexiglass, nor if silicon would bond the glass to the rubbermaid. Thoughts guys?