My 20 year old MercedesBenz has 2 batteries, 1 in front to start car, 1 in rear for everything else.
It has a dual battery charging isolator to charge the front battery.
There is a battery boost relay to boost if either battery is low, or alternator dies, the other battery
can provide extra power.
There is a large 35x50mm? 4700u f capacitor in the a front fuse box in front between the alternator and
rear battery.
The 20 year old capacitor now measures around 5600.
To help protect the battery isolator, I want to add a capacitor between the rear battery booster relay and
battery isolator, and would like to add a 2nd capacitor on the rear battery side.
I the car sits for a few weeks the rear battery will drain and the booster relay turns on, I assume there
is a large voltage spike when it connects and disconnects.
Rear battery is on a battery maintainer, unless I forget to plug in or it gets unplugged.

See attached picture, any suggestions?

 

The primary purpose of the capacitor is to reduce electrical noise from the alternator output, which could affect electrical systems within the vehicle (particularly electronics and audio systems) – so adding a second capacitor as you propose will gain very little.

 

With a system that old, and the capacitor that old, I suggest measuring the current drawn from from each battery when everything is switched off. There may be leakage current that is a problem. High value capacitors do lose capacitance and they sometimes do increase leakage current, and both of those reduce the effectiveness of whatever benefit they were intended to provide.