The dual alt setup is a little different from the single. Both batteries are still in parallel, and get charged equally. However, it should only charge from ONE alternator until your electrical load exceeds the first alternators output, at which time the second alternator gets a signal from the compter to start supplying voltage.
I dont think its something your run of the mill parts store can check. This is more of a job for an OBD reader that can really get into the computer and look at more than just codes. Auto-X-ray, and Autoenginuity come to mind. Ford and possibly international would be the only other guys that can check the signal from the computer that might be kicking on the second alternator and over charging the bats.