If you plan to use the iPads in "Unsupervised" mode, you don't have to delete the existing apps. You can simply add future apps using Apple Configurator on the "Prepare" tab. On the Prepare screen, be sure that Supervision is Off, iOS is "No Change," Restore should be "Don't Restore Backup." Click on the Apps tab and place a check in the box next to the app you want to install (you need to first download the app in iTunes, and then import it into Apple Configurator for it to appear in this screen.... click the "+" a the bottom of the window to add apps).
If you want to "Supervise" the iPads, it will wipe the iPads. However, you could always re-download the apps onto each of the iPads using their individual Apple IDs. This would be like using the "Layered Ownership" deployment model where multiple Apple IDs can be used on a single device.
Hope this helps!
~Joe