automatic charging relay for dual battery setups interference in speakers

i have recently installed a dual battery setup in my 21 ft boat. i have 2 6x9's 4 5.25's 2 1000 watt amps and 3 10 inch subwoofers. The batteries are a deep cycle and a high cranking amp just for starting. in between the two batteries I have an ACR and a perko switch. my problem is that any time the alternator or on onboard battery charger is charging the stereo starts popping regardless of the volume level. i know the ACR is causing the interference but i don't know what to do about it. any help will be greatly appreciated!