I think you'll have to first find out if your system USED to charge both battery groups on the engine alternator. If so, what's gone wrong. You can measure with a volt meter, at rest, charged batteries should read about 12.7 v. Under charge, the reading should go up to 13.4 v or more. There are 'boxes' you can add if you never had the capacity to charge both groups while under engine alternator, generator, or shore power. One such box is Trik-L-Start.
Ultra Trik-L-Start LSL Products
Check and see if your battery boost switch works, it connects both House and Chassis batteries for emergency starts. The same relay is sometimes used to connect the batteries together when there is charging available. If it's bad, replacing or repairing that should allow all your batteries to charge again. The Trik-L-Start is usually only added when you don't have a built in system.