Are you looking to collect files from the devices or make sure the files are removed and the iPads are set back to the original configurations every day/week, etc?
collect the files from the iPad's!
I'd recommend a LMS (learning management system). If your district uses Google Apps for Education, you can use Google Classroom. My district uses Schoology. My wife's district uses My Big Campus. You can also use Edmodo. There are other options available, but those are the ones I know about.
The way it works is this - teacher creates an assignment through the lms website. Students log in to get the assignment. Once they complete the assignment, they upload it using the LMS app and turn it in.