Lee
"people are now telling me I should not be using this aux charging setup and should be going from my start battery to my house battery via a VSR"
This is how my twin motor set up was wired by a marine electrician years ago. He actually builds a automatic battery controller that he wired into the boat. No switches or controls that I have to operate. It simply connects the house battery to one of the start batteries after the motor has started and disconnects the house battery
a when the motor is started (to protect the electronics in the boat and
b if the house battery voltage drops too low so the start battery always has sufficient power to start the motor.
Simple cheap and after 17 years use i can say its durable too.
Who ever told you what they told you is probably on the right track so sticking with a system that seems to have issues does not appear to be the way to go IMHO
Cheers
Chimo