So I backed up my iPhone 5 to iTunes. Plugged in my iPhone 5S and hit restore from iPhone 5 backup. After it was finished none of my apps were there. Plugged in my iPhone 5 and figured I didn't transfer my purchases. Did that and plugged in the 5S. It starts transferring the apps but they aren't organized in folder from as it was on the 5. I thought when you backed up your phone it made a "mirror" of it. What's the best method so next time it will be more seamless.