An HVAC module having a reconfigurable bi-level duct system is disclosed. The air duct includes an air duct inlet in fluid communication with the HVAC module, an interior wall dividing the air duct into first and second air passageways, a bypass port enabling fluid communication between the first air and second air passageways. A downstream control valve disposed adjacent the bypass port and is configured to selectively direct air flow from one of the first and second air passageways to the other of the first and second air passageways. An upstream flow control valve is disposed adjacent to the inlet of the air duct, wherein the upstream flow control valve is configured to selectively direct air flow from the hot and cold chambers of the HVAC module to the first and second air passageways of the air duct.