I Installed a small amp and sub and have been noticing a loud click from my starter battery after the Install, I pulled a ground off the negative of the starter battery, you think this is the reason?

It clicks when I start the car and maybe 20 seconds after I turn the car off
Everything else seems to be normal

 

Am sure you don't mean eliminated/removed a ground wire from the starter battery when you say 'pulled'.

So you must mean you are using the ground of the starter battery so i'd just move both the + and - to the other battery and see what happens. Remember to have a proper fuse on the + side around SIX INCHES OF ACTUAL CABLE LENGTH away from the + of the battery for safety sake.

 

Ya I just jumped off the ground
The positives off the acc batt on the driver side it's fused

I'm going to get a new ground cable and run it off the driver side batt

And see if that fixes it

 

Have a feeling your creative wringing by using one batt for + and the other one for - is the problem.