This article presents two case studies aimed at exploring the use of self-explanations in the context of computational science and engineering (CSE) education. The self-explanations were elicited as students' in-code comments of a set of worked-examples, and the cases involved two different approaches to CSE education: glass box and black box. The glass-box approach corresponds to a programming course for materials science and engineering students that focuses on introducing programming concepts while solving disciplinary problems. The black-box approach involves the introduction of Python-based computational tools within a thermodynamics course to represent disciplinary phenomena. Two semesters of data collection for each case study allowed us to identify the effect of using in-code comments as a self-explanation strategy on students' engagement with the worked-examples and students' perceptions of these activities within each context. The results suggest that the use of in-code comments as a self-explanation strategy increased students' awareness of the worked-examples while engaging with them. The students' perceived uses of the in-code commenting activities include: understanding the example, making a connection between the programming code and the disciplinary problem, and becoming familiar with the programming language syntax, among others.