This is a diagram on how the 6V and 12V batteries should be connected for use in the RV trailers. If you connected the 6V battery charger to just the + and - terminals of ONE 6V battery then all is ok....
I don't own a 6V battery charger so I always connect across the 12V and ground path just like the converter/charger does when connected to shore power.
The downside of what you may have done is that only ONE of your two 6V batteries received some charge and the other one has not. In this case since you have only one 6VDC charger it is probably best to trickle charge both 6V batteries at the same time using the 12VDC setting on your charger from the 12V and GND connection point..
I am not a fan of using the trickle charge method is you only do it for a short period of time. We have found out when camping off the power grid just charging the batteries for an hour or so for instance and then start using the batteries right away they will NOT perform to their specifications and will almost immediately drop down to the 50% charge state in just a short run time. Continuing doing this procedure will eventually harm your batteries.
We always follow the rule of not letting the batteries drop below the 50% charge state which is approximately 12.0VDC and then re-charge in a timely manner back up to the 90% charge state (appx 12.6VDC) in a short three hour time period using smart-mode charging technology. Doing this the batteries seem to perform at their specified performance curve. You can do do this 50% to 90% charge cycle for around 12-14 times before you must do a full 100% charge cycle which will take about 12 hours to do using smart-mode charging technology. Where we camp of the power grid this is usually not an option for us as the camp ground does not allow us the run the generator for that long of time so this is usually when we pack up and come home.
However if left sitting at home for a week or two then the trickle charge method would be ok to do but I would use 12VDC method so that both 6VDC batteries would receive the trickle charge.
just my thoughts