8.1L secondary battery problem. Bad alternator or voltage regulator?

My 2006 Silverado 8.1l, wore out the secondary battery which sits on the back firewall passenger side after 40K miles. The battery was overheating and ready to explode. I changed both batteries out and now 2 months later the new battery by the back firewall was leaking acid/water. I got it replaced but I'm afaid I might have an over charging issue. I have to get it checked but I wonder on this year/model if I would have to replace the whole alternator or might I be able to replace just the voltage regulator? Is the VR separate from the alternator? I got a free alternator check at Advance and the read out came back with no problems, charging fine, I imagine that was not a full test of the system though, just when they hook up the generic tester machine. Any advice? Thanks!