In our app we have UIScrollView above CAEAGLLayer. UIScrollView contains some UIViews (red rectangles). In CAEAGLLayer we draw white rectangles. Centers of white rectangles
In fact, you can't synchronize them using current APIs. MobileMaps.app and Apple Map Kit use private property on CAEAGLLayer asynchronous to workaround this issue.
Here is related radar: http://openradar.appspot.com/radar?id=3118401