Thanks everyone for these posts, I feel much better about my complete failure to get Configurator 2 to work and reverting back to 1. I also had the issue of using free apps from iTunes but using the VPP account is an issue for me. I work at University and our VPP account is managed by finance. I do not have access to it and so cannot use it for C2. Background is it took me almost 6 months to get this system set up with all the red tape and am not really keen to start all over again.
My second issue is that I set up folders and bookmarks, make a backup and then deploy that to the rest of the devices. This enables me to have a number of images that I can deploy depending on user requirements. With C2 this is impossible as restoring a backup deletes the entire device and unsupervises it. I have yet to discover a way in C2 blueprints to create folders or add bookmarks.