Most battery configurations will be similar, though some have a couple more house batteries. Here is a photo of our C9 bank if it will help. The two 12 volt chassis bats on the left side are in parallel, then the four 6 volt coach bats are wired in pairs in series so each pair puts out 12 volts, then those two 12 volt sets hook up in parallel so there is plenty of amp storage capacity still being pushed by 12 volts total. If you happen to use 12 volt deep cycle house bats rather than 6 volt ones, then none are hooked together in series - all are parallel.
To get two 6 volt bats to add together for 12 volts, i.e. - in series, you must connect them with a short cable between one's positive post and the other's negative; that way the 6 volts of one flows into the other and produces 12 volts at the other end. In parallel, the 12 volt sources (whether individual batteries or two 6 volt ones wired additively in series), are hooked together positive post to positive post and negative to negative. In my photo, anything with a red sealing sleeve on the end is at a positive battery post.
You may be hooking your 12 volt starting bats together in series, with 24 volts output. Make sure you don't have the positive of one chassis battery wired to the negative of the other. If you've had the battery wiring apart, and reassembled, then misassembly is likely the problem. But there could be a hard-grounded starter or alternator involved instead.
Joel