Bob, I have my propane burner at the back of the stone tray, per Willards instruction. This allows the heat of the flame to rise over the pizza and also to heat the top stone. The one draw back I find is that the bottom stone heats more in the back than the front or sides, hence the steel plate that the stone sits on turns, in my case manually. I had been experiencing hot spots, burned areas, on the bottom, which I now believe to be because I was not turning the bottom stone frequently enough. I pie could also be turned on the stone but that does not keep the stone temp even.
Mark