We try and supervise all student iPads. Admin and Teacher iPads are not supervised. We use Configurator to set them all up and enroll the devices with Configurator supervised or not. You can deploy apps later using the JSS and they will remain on there after updating or refreshing those iPads in Configurator so long as you "uncheck" a box in the Configurator preferences. In preferences uncheck the box next to "Remove Apps and Profiles Configurator did not install.
When you supervise and install apps on an iPad in Configurator, those iPads are forevermore dependent on the computer you use to set those iPads up with. We call those computers provisional nodes, and we require each site to purchase a dedicated provisional node. This way we can setup each sites designated amount of iPads on their own provisional node. We prefer to then use Apple Remote Desktop into those provisional nodes to continue installing any new app purchases with Configurator rather than using the JSS. This way the codes are not consumed.
On the unsupervised iPads we use an in shop computer with configurator to enroll the devices, then later push out new apps with the JSS.
Hope this helps or gets you thinking.
Chuck
