I have a 50W panel & controller I would like to use to maintain two batteries (of the same size) in two separate ATVs (of the same make & model) stored in a sea container for the winter. My question is if one battery is weaker than the other, will that cause the controller to continue to charge the stronger battery causing possible damage from an over-charge
Simply put if the two batteries are hooked together they will act as one and the charger will 'see' the common voltage and charge to that level. The higher level battery will tend to help bring the lower one up to the common level the same as if you were boosting your car.