This is kind of a tricky one, even though it's an incredibly common use case.
1) One idea is to have an empty root view controller as your detail and it handles managing segues under the hood to quickly segue to the detail view you actually care about, utilizing the "replace" segue. This should "technically" fix having the "back" button at the top left and still allow you to pop to root and not have it show the empty controller. Haven't tested these though, so I'm not sure.
Edit: In Xcode 6, the "replace" segue is conveniently handled by a "show detail" segue which is used specifically for this type of view handling on Split View Controllers. I recommend using this method exclusively in new projects. See sample code.
2) The other idea is to have separate navigation controllers in your storyboard (one connected, the rest all stranded). One for each detail view type and tapping on the master menu will simply swap the navigation controller for the detail view to the one you care about.
Code similar to this in AppDelegate:
self.detailNavigationController = [self.masterNavigationController.storyboard instantiateViewControllerWithIdentifier:@"MyChosenNavigationControllerStoryboardId"];
self.splitViewController.viewControllers = @[self.splitViewController.viewControllers[0], self.detailNavigationController];
self.splitViewController.delegate = (id)self.detailNavigationController.topViewController;
The downside to this second way is that in memory tests, it doesn't appear that swapping a new nav controllers in frees up all of the memory that the old nav controller was using. So it's good to use for simple apps but not for anything crazy complex.