A corporate discount cannot be modified by a sales rep. Not easily, anyway. I have also never seen a discount at only 3%.
As suggested call in or go back to the store to get it taken care of. Me? If a rep was rude to me I would not work with them. You are not tied to anything until you pay. I would have walked away and come back another day or asked for someone else. It is no secret that VZW reps make a commission.
As far as syncing, you can plug your old iPhone into the computer and sync through iTunes and then plug the new one into the computer and restore everything to the new phone. This takes far less time than iCloud and has been a feature of iPhone since its inception in 2007. Of course, if you traded in your iPhone it has probably already been reset to factory settings and sent away. You'll not get it back in this case.