Sounds like you hooked it up right then. The pressure line from exhaust goes to the main tank, then the outlet on the main tank goes to the inlet on the header tank, then the outlet of the header tank goes to the carb...you will not get two exhaust lines setting it up in series like that.
Refill the main tank when it empties, dont let the header tank drain. Well with your setup you can but a lot of guys run airplane fuel tanks as the header and they are a pain to fill and the purpose of the header tank mod is to supply fuel from a vessel that is constant, that way it will work at its best.