The thing to understand is that layer animation is just animation; it's merely a kind of temporary "movie" covering the screen. When the animation ends, the "movie" is removed, thus revealing the true situation. It is up to you to match that situation with the final frame of the movie.
UIView animation does this for you, to a great extent. But layer animation leaves it entirely up to you.
Thus, let's say you animate a position change; doing something so that the layer or view actually is where you animated to is completely up to you.
The usual thing is to perform the changes yourself as a separate set of commands. But be careful not to do anything that might trigger implicit layer animation, as this will conflict with the animation you are trying to perform explicitly.
Here's example code (not related to yours, but it does show the general form):
CAAnimationGroup* group = // ...
// ... configure the animation ...
[view.layer addAnimation:group forKey:nil];
// now we are ready to set up the view to look like the final "frame" of the animation
[CATransaction setDisableActions:YES]; // do not trigger implicit animation by mistake
view.layer.position = finalPosition; // assume we have worked this out