If you are using my mod, or the other mods here, then you have connected both battery's together (+ to +, - to -) then when you charge the battery where in the phone or external charger you charge both battery's, this is parallel battery tech 101, of course this works best with 2 similar battery's, if you use say a 500mAh and a 1320mAh then the 500mAh could get drained beyond it's limits or it could drag the 1320mAh down with it fast, or if the electronics works and cuts it off then it will work as it was intended.

Edit: HtheB i have added the discount code at the buy mugen cover section.