The #1 rule of grounding is that you want to keep your grounds short. A long ground can be ineffective.
The best thing to do in your case was to use bare metal in the trunk area to ground the grounding block so you could then connect the 3 grounds to the block. The battery wasn't needed to ground the subs. Many people ground on one of the strut towers (taking off a bolt from the strut and placing the ground terminal there) or they ground to a bolt that's behind the seat when it comes down. Those are the best places to ground in an N body.
The point of the big 3 is to have a better ground. The only long wire in your big 3 should be alternator (positive) to battery. I also hope you didn't ground your alternator to your battery. You ground your alternator to the car's body and you ground your battery to the car's body. Many people use the stock ground point and attach the new ground.
I hope this helps you out.
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