The to[p tank would have to be sealed airtight, and the inlet aon outlet intot he bottom tank would have to be below waterlevel at all times.. Then the top tank couldn't drain into the bottom tank, any water to fall from the top tank would have to be replaced by water drawn up from the bottom tank since the top is airtight... would create a vacuum effect.
that's absurd.
i'm not even sure what you imagine the OP doing, but he isn't drilling the bottom of his tank or anything like that. a standard overflow that is maybe 2 inches from the top of the aquarium would safely run a safe amount of water down to the lower tank. it would overflow at whatever rate the pump pumps at.
my suggestion though, like some others have said, is to put the fish in the top tank. the bottom tank will be fine with just plants and that's where you'll be putting your pump anyway. throw a prefilter on the pump and the tank with fish will be getting clean water instead of having to live in water that has not yet just passed through a filter. sponges and most filter media will have more surface area than plants so it's best to run it that way (mechanical then chemical) anyway.