That means you're running the amps off the main battery, not the aux. Are you going to use a switch to swap the power over when the engine is off? You could do it with a relay. When ignition power is on, the relay picks power from the main battery, and when it's off, it takes power from the aux. A single SPDT 40A relay would do the trick. Look at the numbers underneath and connect as follows:
Pin 30: to the amp
Pin 85: to ignition on (any source that comes on with ENGINE on, not just ACC)
Pin 86: to earth
Pin 87: to main battery (so pin 30 is energised when pin 85 is active)
Pin 87a: to aux battery.
Don't forget that any and EVERY cable that comes off the battery NEEDS an appropriate fuse.