You may find it interesting to observe how Eric Mazur, professor at Physics at Harvard, determined that his own teaching methods were inadequate. The whole talk is fascinating in its description of an alternative teaching approach he has developed; However to your question I think the important point is the method used by Mazur to initially observe that something is not going well at all.
Starting at 00:04:00, Prof. Mazur describes the initial criteria which led him to believe he was doing a good job (success at the end of term questionnaire). Then - more importantly - starting at 00:06:30, he describes how a survey of conceptual understanding helped him realize that something was very fundamentally wrong. The specific proposal is running an identical pre-course and post-course test which attempts to examine the quality of basic understanding of the concepts.