[jclark003]

If you have a digital volt meter you can start by checking voltage at each battery bank. If charger is working properly you should see somewhere around 13.5v - 13.8v with charger on. If you don't see that check the breakers and fuses on charger if so equipped.

Seems odd that both banks are being drawn down. If you have a battery interconnect switch make sure it is off/open to help isolate and locate the source. From there as misdirection stated putting a D.C. Amp meter in line and shutting off circuit breakers should help find the problem.