Due to the rapid growth of e-Learning contents, especially videos, published online, the usability of tools that help students keep track of such contents along with their thought traces is an issue. We addressed the problem by designing and building a web-based semantic annotation tool called NotesKB. Through technical and theoretical lenses, we aim to discover and improve upon the usability of such tools. The usability of NotesKB is evaluated and compared with two other predominant note-taking methods, namely Pen and Paper (PnP) and Microsoft OneNote. According to the SUS test scores, PnP is the most usable while NotesKB was the most preferred when students were interviewed. We have reaffirmed that cognitive load is key to design e-Learning systems and that note-taking tools with semantic capabilities need to help users learn how to use the greater power available.