We have auditing turned on and use it to push out config to our controllers. To get you started, your master and all its locals should be in the same AMP Group. In the AMP group, you define what ap-groups, ap-names, as well as any user-roles/policies that are not tied to aaa-profiles, should be on that controller cluster. You importing the master's config into AMP is the right thing to do, and should hopefully result in a 'Good' state. Since the locals get their config from the master, they, too, should be in a 'Good' state. However, if they are not, do NOT import their configuration right away, as that could cause the mismatched state you describe.
You need to look at the mismatches on the local and see what is causing it. It could likely be some local configuration applied on the local controller that Airwave simply does not know about. For example, some of my local controllers have a bandwidth contract applied on a vlan interface. This is not on the master, so I had to ensure it was added under that local controller's "Manage" page.
I hope this helps. If not, you can always run the configuration audit report, export as PDF, and post it for assistance.
The configuration auditing is great, and 7.4 will be even better allowing for you to maintain your network in a "monitoring-only" mode while still allowing for schedule-able one-time pushes of configuration.
It's quite powerful, and I'm puzzled why it is not used more often. I, too, am a "CLI guy", but with a network as large as ours, I can't imagine not having Airwave . . . it's basically servicing us as a 3rd full time employee. :-)