Your description makes my head spin... 
Try a simple test. Start with fully-charged batteries. Temporarily disconnect the alternator feed to the auxiliary battery. Turn on all your stuff. Start up the car and race the engine to cruise rpm. Do you hear the whine?

Try a simple test. Start with fully-charged batteries. Temporarily disconnect the alternator feed to the auxiliary battery. Turn on all your stuff. Start up the car and race the engine to cruise rpm. Do you hear the whine?