let me clarify this a little...
multiple battery systems are an interesting thing,it's like this...when the battery switch is ran in the "all" or "both" position,you're drawing from both batteries,meaning,both batteries are being discharged,they're parralleled...now,with that,if one of those batteries goes bad,it's gonna take the other battery out...a discharged battery will discharge a fully charged battery-i promise you that...
electrical systems are a little tricky sometimes,the new electronics are very voltage sensitive,a good example of this are the raymarine sets,the "c" and "e" series...these sets require a pretty constant voltage supply.
it's a real good idea to have a dedicated power supply as well as a ground for the electronics...
i like multiple batteries ina seperated and dedicated set up,meaning the engine battery is seperated and electrically isolated from the engine battery.by having this set up,when you're drifting or on the anchor with the gps on,the stereo on and the vhf on,you're not drawing from the engine battery,you're drawing from the 12v system battery...therefore,you have no fear of the engine not being able to crank when it comes time to run home...when you fire the engine up,it recharges both batteries...like this...i use a blue seas "acr",it's a sense relay,it sense voltage at both legs,when the voltage at one of the legs is 13.2v or higher,the relay grounds,allowing both batteries to charge at the same time...when the voltage at one of the legs drops below 13.2v,it opens...pretty simple stuff huh ???
i set the system up with simple on/off switches...pretty fool proof stuff...
the problem this gentleman is experiencing could be caused by weak batteries,it also could be caused by the way the electronics are wired...sometimes the "feed" wire for the 12v system is a little too small to carry the load for the entire system,remember,the longer the wire run,the larger guage wire is required,due to a volt drop across the length of the wire...
i could go for hours explaining how to wire a boat correctly,i've lost count of the boats i've set up with the seperated and dedicated systems,and i've lost count of the problems with electrical systems i've seen...
i only explain what works for me,and how i set up customer's boats...