Here is how I wired my ATS with help from diagrams and folks here to get the "best" way for us.
http://forums.goodsamclub.com/index.cfm/fuseaction/thread/tid/29316554/gotomsg/29335313.cfm#29335313Key features:
1. Inverter can be turned on, but the ATS will switch with priority over to shore power/generator power via the camper's main cord.
2. If shore power/genny is not available, the ATS switches over to Inverter 120v power feed for the camper
3. Additionally, the shore power/genny side of the ATS powers a 120v receptacle I added that the new converter/charger plugs into. So the battery charging and 120v to 12v converter circuits are only powered when plugged into shore power or generator power
My invert does have a "bypass" mode that is supposed to act like ATS, but a separate Automatic Transfer Switch seemed the better choice overall.
Here's my wiring diagram from the link: