RV Repair: RV Repair, 12 volt batteries, trouble shooting guide

Question
Two questions.  I have a 1990 Prowler Lynx 16' trailer.  On my last trip I heard a loud bang/pop type noise from the left rear of the trailer.  The only thing working there is the water heater.  It was in use and the flame was light blue in color and burning strong.  It worked fine the rest of the time.  The water heater is a Automatic Storage (Atwood) model #G6A6.  I also had a problem with my heater, A Hydroflame (couldn't find the model #), It would heat up, but when it tried to reheat it would make a clicking noise run a little shut off and repeat.  It appeared that the burner was not lighting, however if I cranked up the thermostat, it would light.  Any ideas?  
How about a third question, what do you like better 2-6 volt golf cart batteries, or two 12 batteries?  Thank you for any help.  

Answer
I am only guessing but it is possible for the water heater to make a loud pop when it ignites late, which is possible under driving conditions. The gas would fill up the chamber then ignite. I would have it looked at though just in case. I will look at some of the service bulletins on your model. On the heater I would check the gas pressure and the limit switch. Here is a link to Atwoods trouble shooting guide. http://www.atwoodmobile.com/Service/Trouble/dsi.cfm
If you are talking about the batteries for the RV I would use 2 12 volt batteries, there is nothing better than having plenty of amperage.