help with hooking up two batteries

i have the battery under the hood and the one in the back i have it hookd up from positive terminal under the hood to positive terminal to the battery in the back and have the positive terminal on the amp hooked to the same spot on the battery in the back for the negative side i have the amp hooked to the negative terminal on the battery thats in the back and from the battery to the frame of the vehicle i was just wondering i get a drop from my alternator about 1 to2 volts when the speakers hit hard with the way its hooked up is that normal or is that going to hurt my alternator in the long run thanx any tips would be greatly appreciated.