Background: Many empirical software engineering studies use students as subjects and are conducted as part of university courses. Aim: We aim at reporting our experiences with using guidelines for integrating empirical studies with our research and teaching goals. Method: We document our experience from conducting three studies with graduate students in two software architecture courses. Results: Our results show some problems that we faced when following the guidelines and deviations we made from the original guidelines. Conclusions: Based on our results we propose recommendations for empirical software engineering studies that are integrated in university courses