The quickest way I have found to get devices in the correct pre-stage is to Unassign the devices in DEP > Refresh DEP within Jamf > create the pre-stage enrolment and select "Automatically assign new devices". You then Assign the devices again in DEP to your Jamf and refresh DEP. This will move all the iPads into the prestage enrolment that you just created. Works best if you know the serial numbers.

@RLR huh, that is genius. I will it a shot!

EDIT: Worked like a charm. Surprised how long it took but they all got in there with their little boxes checked!!
Thanks for saving me from those 1420 clicks!!

How would you work this if you have multiple prestage enrollments?

One enrollment at a time. Do X amount of devices. Turn off Automatically Assign from 1st prestage, turn on Automatically Assign on the next prestage. Repeat.

You'd have to do a set amount of iPads at a time for that specific prestage.

This now takes longer to do as Jamf have removed the ability to manually refresh DEP information. There is now a maximum 5 minute wait on DEP changes. There is a feature request to have the manual refresh button added back in. The best solution would be to allow some sort of csv file upload to control DEP prestages.