Chunk,
The only part of ATA training that is taught by airline pilots are the ground schools (Basic Indoc, CRM, General Systems, RJ Systems, and the RJ Sim).
All of the flight training is done by CFI's, exactly like every other flight school.
Some of our graduates have been furloughed by American Eagle and are now instructing at ATA. They said that the ATA ground schools were a huge help in preparing them for ground school at Eagle.
I haven't gone through the RJ sim yet and I'm not sure about the logging of that time. I'd be willing to bet that it can be logged as simulated instrument (if applicable) and dual received, though. Regardless, I've sat in on a couple sessions and it is worthwhile training. The instructor knows his stuff and really gives the students a workout.