It sounds as though there are two methods of filtration used in this particular aquarium- canister and UG (underground) filtration.
I'm not certain, but I'd guess the water is sucked down underneath the aquarium, where it passes through the canister filter + media, and then gets pumped back into the aquarium.
As for the UG filter... the waste passes through the filter grates located underneath the gravel, and the water gets sucked up the filter intake tube and pushed back into the tank.
A UG filter is good for biological filtration (the gravel is the bacteria bed, in this case), while canister filters are good for mechanical and/or biological filtration (depending on what filter media is used).