2 batterys 1 bad

Hello, 

I have a mustang that has a custom box built in the trunk that also covers 1 optima battery and i have another optima battery under the hood. I was in a car accident and my car sat around for 3 months until i was able to fix it. Now that my car is fixed ive replaced the battery under the hood since it was bad. Whenever i dont drive my car for lets say 8 hours and try to start it the car needs to be jumped. I checked my high output alternator and that is good and the battery under the hood is good does anyone know if the battery in the trunk is bad would that affect the other battery that i have and cause a drain on the other battery? I am in the process now of checking the battery in the trunk its just a pain to get to and wont have time to change it for awhile any help would be much appreciated thanks in advance!