The way you setup view controllers doesn't change when you use the new custom animated transitions in iOS 7. So you would still setup the view controller (including setting the transitioningDelegate) in prepareForSegue if you're using storyboards.
See the following sample code for examples of custom animated transitions using storyboards. It's an implementation of the sample code for WWDC Session 218: Custom Transitions Using View Controllers. Look at SOLViewController.m to get started.