Dual AGM battery setup

[LoganDG]

So Battery 1 this is one that is hooked up to the alternator so it’s going to be in the engine bay and battery 2 is gonna be in the trunk, would it be safe to run these in parallel then take the positive terminal from battery 1 connect it to my amp then take the negative terminal from battery 2 and connect it to my amp. I was curious because the negative run to the amp is going to be much smaller.

[audiofanaticz]

Hook the amps positive and negative to the closest battery (IE the one in your trunk). 
Current flows from the path of least resistance and that would be the battery in your trunk and not a botched collaboration of the 2 in some big ol loopty loop.
Just connect both batteries together in parallel positive to positive and negative to negative with the amp(s) connected to the nearest battery.