Application of Theory, is sort of shaky. Basically, our theories are created so that, they are independent of the real world (sort of), but, application is obviously warranted. Here, pupils get confused because theory does not look like the practice many times.
Explain the theory from practical perspective. Tell them how it mixes with reality, rather than introducing it most abstractedly. Application follows by this connection naturally.
If pupils have problems yet, let them work through some problems with teacher guidance. Because, it strictly does not matter if pupil can apply the theory or not, remember, theory is just something stand-alone and abstract without worrying about practice.
Let them learn this slowly, and happily, because it is not theory, it is about practical application. Often times, the model to reality mapping is not taught to pupils, and application problems are thrust upon them.