in need help on gettin that base out of my trunk without ruining the structure to much of my 89 bonneville and I also need to know if is possible to run a second battery and how to do so.

What exactly are you trying to do again?

For audio, I wouldn't install a 2nd battery... instead install a capacitor.

I dont know much about that body style, but it sounds like you might wanna get ahold of a welder if your as serious as you sound about audio

remove the rear 6x9'*. That should let bass in much more into the cabin. For those who don't know, there is a solid sheet of metal between the trunk and cabin of the Bonneville. here is a picture of this in my 88 LeSabre I had back in the day:

you need a battery isolator

ummmmm...not on mine...

for the pre 92+ they are not that way