Each of the both center tank pump feeds into one side of the fuel system. Since the center tank pumps have a higher output pressure, as long as they are used no or little fuel from the wing tanks will be used to feed the engine. If only one center tank pump is running the wing tank on that side will remain full (or close to full) while the other engine is fed from its onside wing tank and its level will decrease, creating an imbalance.
Just one question: What has the APU to do with it?