Restoring Configuration Profiles on iOS 7

I have a 5S that I had to replace. I had both the supervise profile and also a restrictions profile installed. I backed up to iTunes with an encrypted backup, but when I restore the backup the profiles do not get restored (which is how I believe it is suppose to work).

However if I either prepare the phone first in Apple Configurator or restore the backup then prepare the phone the profiles cannot be installed without wiping the phone. How do I go about installing the profiles without having to setup the phone from scratch and losing all of my iCloud data like I had to do the last time?

Thanks in advance.