Apple Configurator - Restore failed- is there a fullproof workflow?

Hey all,
I have had to switch out machines in which I am running configurator off of. I have up to date versions of IOS installed on the machine and devices. I have the latest version of apple configurator installed as well. I am installing close to 150 apps on iPad's and I have to put everything in to folders. As far as I know there are only two options for doing this.
Option 1
Do it through iTunes (The easy way)
Option 2
Load all the apps on an ipad using configurator and to drag all the icons with your finger and make folders (the hard way)
I went ahead and made a master ipad image in itunes and then realized when I went to supervise an ipad that everything would be gone (Doh)
I have since SUPERVISED an ipad first and then went in to settings and disabled auto refresh. I then took this supervised ipad and brought in to itunes.
I placed all of the apps on the device and moved them in to a folder. I have created a perfect ipad image again and created a backup in configurator.  No matter what I do I can't get a backup of an ipad to succseffuly restore in configurator. The ipad goes through the restore process but it turns off and doesn't turn back on. Is there a fool proof workflow out there right now?
I haven't tried Option 2 as it is a painstakingly slow process. But it does leave Itunes out of the equation so would that help?

Well it appears this is no more than the problem most everyone is having with to many application icons...

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