The paper presents two complementary approaches in using Web technologies to address typical difficulties arising in distance learning of theoretical CS courses such as Automata and Formal Languages (AFL). The first focuses on reasoning-related problems that are addressed through pro-active tutor-driven discussions in a course netforum. It is based on an analysis of typical mistakes and misconceptions revealed in discussions of a set of appropriate examples developed especially for this purpose. The second approach addresses problems relating to the creation, validation and transformation of computational models; it is based on the use of software tools for hands-on exploration of the concepts and algorithms studied. Tools developed for distance learning of AFL are presented; they use visualization and animation to make mathematical models live and tangible. Integration of these tools into the asynchronous distance learning process is discussed.