oo: the only water that will go through your overflow is the water that is pumped into it.
think of it this way, if you were to fill a glass with water, and then keep pouring water into it, it will overflow... if you only pour water in half as fast, it is still going to overflow, but only half as much as originally, that is, water isnt going to flow out, that isnt extra. water will not drop below the rim.
this is the same principle with an aquarium. an overflow works based on water level in your tank. if the water level is being pushed up fast, more water will move through the overflow. if it fills slower, or stops filling, there will not be as much or any to move through the overflow.
so in a round about answer, no your tank will never drain due to a smaller input than output.
as for the refugium filling up, it too will have an overflow. the total volume of the tank will not change, so once you get it set with how much flow you want through specific areas it will just go on its own. you are not adding more water to the system, so the overflows will just drain water as fast as it is pumped into it (this is assuming that the overflows are large enough.
