I've considered doing something similar a few times, but I have kids and they are destruction-y.
If I'm not mistaken the bottom portion of the front glass of the inner part doesn't extend to the bottom of the tank, is that right?
If that's the case, you're going to need a powerhead of some sort to mix the water. You could try using the pump from one of those desktop fountains that you can buy at Target/Walmart. The flow rate on those is small enough that it shouldn't cause any issues, and it ought to come with tubing that connects the pump to the fountain fixture. You could also try something like an Aquaclear 10 turned down to its lowest setting. I use that in a 3 gallon jar without any issues.