It's a good design in general theory. Very good point about draining their Jobo, an air-vent to move water from the lower tank to the upper tank would help a lot.
I don't currently have a rain collector, but I helped a friend set-up one at his house. The barrels were set-up vertically rather than horizontally. He drilled a 3/4" hole 4" up from the bottom of the source tank (tank that the rain water drains directly into) and 3" up from the bottom of the supply tank (tank that you draw water off of) This provided a place for debrie to settle in the source tank with minimal loss of capacity.
For Air venting, he connected a top-side hose from the supply barrel to the source barrel. The source barrel had a spout about 1 1/2" up from the bottom, allowing it to be virtually completely drained, leaving 4" of water in the source tank.
About 2 years ago, we expanded the system to add 4 additional barrels each with 2 holes cut 3" up from the bottom, providing about 300 gallons of useful storage.
The barrels are on a stand about 4' above the ground to provide for gravity flow.