What is an effective note taking procedure?
You can keep 2 sub notes per topic, one of them can be composed of excerpts lifted from books/internet, the other can be on your thoughts/summary of the material. 
You can use a standard numbering scheme for both notes to keep track of content; e.g. in notebook 1, 1.2.4 can be Geography>Rivers>Nile in both sub notes.
Take care to paste searchable text and not images of text, for ease of later access.