Charging problems

I am having issues with the electrical system which I am not too familiar with and after reading some of the questions on this website, I have learned a lot about the elec. System, and I am hoping I can get help here figuring out my problem. I own a 26 ft. 2005 Tioga on a Chevy chassis, and in 2011 the batteries were going bad (from lack of maintenance) so I bought 2 24DC’s from Walmart. Being unfamiliar with the batteries in the RV, I thought they were the same type so I hooked them up in series, after a few sparks I realized that originally it had came with 2 6 volt batteries instead of 2 12’s so I hooked them up in parallel and all was good (except for my grey and black water indicator lights on my monitor didn’t work anymore and a replaced GFI in the bathroom). After 3 years the 2 12’s started failing, they would only hold a charge for about a day, and then I would need to run the engine for a few hours to charge them, (that is when I noticed the generator was not charging them) so I bought 2 Interstate 6 volt GC2’s with 232 Ah, and after I installed and connected them in series they had an initial voltage of 12.28. The problem I am having now is the only time I get a charging voltage is when the vehicle engine is running, I checked the output on my WF 8845 converter with shore power and the batteries disconnected and it was zero. I checked it with batteries connected and it was 12.28. So I started the Onan 4000 gen. and plugged the shore cord into the RV’s storage bay outlet and the batteries still read 12.28, so I started the engine and after about 10 minutes I checked the batteries and they were at 13.34. During all this I noticed the fan on the converter never started but I don’t think I ran it long enough to get hot just warmer. I intend to upgrade the converter to a PD9260 as soon as I can figure out the charging issue. Besides batteries and the 1 GFI I have not had any other issues. So I am wondering if another component has failed like a transfer switch, besides the switches for the aux. batteries and gen. start on the wall monitor, there are a couple of toggle switches on the dash, one to start the generator the other to boost the chassis battery. I am not familiar with the components in my battery box (they look like relays and solenoids) or if there is any located anywhere else. Hope there is enough information for someone to help me. Thanks in advance.