With a relay, either will technically work. I guess its probably a little better to run the amps of whichever battery is closer, but then you have to make sure everything else is on that battery (head unit, eq, anything else that comes on when your key is in the accy. position), if your goal is always being able to start your car.

For your purpose, it makes sense to run all audio off of the main battery, and then just use the second battery to 'jump start' the car, if you run the main one down. This way, your second battery is free from all loads that could be present while running your stereo.

How is the relay wired? Specifically, where does it get its open / close signal voltage from?

Toby