You're definately going to need more plants/cover for the puffers in the top tank. By setting up a tank like this you're basically making a type of sump filter, the beauty of these is that you're increasing the total volume of water hence reducing the possibility of ammonia/nitrites/ammonia going too high, maintainence would also be easier.
The only problems that I can see is that most external filters need to be below the level of the tank as they're gravity fed, the pump only helps the water go back up, if you had the filters at the same level you've run quite a high risk of burning the motor in the filter out. Have a look in the marine section or the DIY as I'm sure there is some info there on Sump filters.
In a nut shell, if you've got the space and money they're a VERY effective setup.