It is quite common for students to do so much reading and note-taking that their own responses are overwhelmed. Their writing and structure is driven by their reading, by other people's arguments, rather than using that reading as a basis for their own ideas. The essays then become loosely structured, descriptive accounts of all that they have read, as their own ideas have not had a chance to be formed. A well-structured approach to note-taking can be a great help in promoting structured thinking and writing later in the process. If your notes are selective and well-organised according to your own research needs, then it will be much easier to find what you are looking for later on, and there will also be much less danger of your own ideas being swamped by the sheer amount of other people's research you have dealt with. If you have thought about how you will select material and how you will structure your notes to suit the purpose for which you are taking them, your own ideas will be better developed and structured.
The ultimate challenge in note-taking is to keep the text's agenda and your agenda quite separate. No book or article that you read was written with the sole purpose of helping you answer your specific assignment. Therefore, each text has its own agenda, and it is important, if your own ideas are to develop independently, not to get too drawn into someone else's reasons for writing. If your notes essentially summarize the text you are reading only according to its own priorities and structure, then your ideas will be driven by the other author's agenda instead of providing you with material on which to base your own.