A process, control system and apparatus for controlling the air side flows to the major components of a fuel processor apparatus are provided. The control system employs a multi-capacity blower provides process air to a partial oxidation reactor and a preferential oxidation reactor. The multi-capacity blower preferably provides a portion of the process air through a control valve to the partial oxidation reactor and the remaining portion of the process air is passed through a flow restrictor to supply process air to the preferential oxidation reactor. The control system of the present invention is simple, low cost and reliable.