I'll repeat Oneilkeys -- the USE/STORE switch MUST be in Use for the house batteries to charge. Also, check with your dealer but the Windsport engine driven alternator should also charge your house batteries when you are driving down the road (USE/STORE in Use) without simultaneously running the generator.
The house batteries will charge with the switch in Use when:
1 - you are plugged in to shore power (charged from the converter), or
2 - when your generator is running (charged through the converter), or
3 - running down the road (charged from the alternator).
Assume your coach batteries and the chassis battery are two separate battery banks. You have automatic circuits (sensors and relays) either in a battery control center (BCC) or a Bi-directional Isolation Relay Delay (BIRD)/Trombetta system. They operate by monitoring the voltage level on a battery bank. When that bank charge reaches 13.1 volts for 2.5 minutes, it will operate relays to isolate the fully charged bank from the other bank. It will then channel charging current to the second bank and again when that bank shows 13.1 volts for 2.5 minutes it will isolate that bank and switch back to the other. The reason the relays isolate one bank from the other is so that the weaker bank does not pull down the charge from the fuller bank.
For a more detailed description about how these monitor/relay systems work to keep both battery banks charged, put the word BIRD in the search function. Here is another link for more information about the BIRD/Trombetta or Battery Control Center:
http://www.thorforums.com/forums/f10...when-3315.html