I have been experimenting with backups and my cart of iPads today and this is what I found:
1. There does not appear to be a way to restrict Settings, Messages, Reminders, Game Centre, and Contacts. This is a huge disappointment for me since Apple is promoting the configurator for use in schools. There should be a way to disable those programs in an educational environment.
2. There doesn't appear to be a way to keep users from changing the wallpaper either. This is another huge disappointment. I have two iPad carts in a secondary school and kids love to change the wallpaper.
3. The restrictions that you can configure using a profile are actually LESS restrictive than if you set the restrictions manually. I applied a backup of a device that had the restrictions set the way I wanted them but because I also installed a profile the profile restrictions took precedence. Furthermore, I could not find a way to keep users from creating a restrictions password and going into the restrictions. They can't change the settings that were set by the profile restricitons via the configurator, but they can still change other restrictions that you can't set using the configurator. For instance, the user may not be able to turn off Find my iPad, but they can turn off location settings, rendering Find my iPad useless!
Applying a backup did enable me to create a layout with folders, etc. and layering the profiles enabled me to create email settings on a per-device basis which I really like. However, I am extremely disappointed in the lack of restrictions capability with the profiles. We are going to have to go in and create the restrictions manually after configuration and reapply them manually every time we update anything using the configurator. It seems obvious to me that Apple did not actually TALK to educators who are using cart setups to get input when developing the Configurator. I am very disappointed.
If anyone has figured out ways to do the things I listed above using the Configurator, or via any other method, I welcome your input!