What is an effective note taking procedure? I've recently started to use the onenote software to keep track of valuable concepts in different fields of interest. I have constantly found myself dubious during the note taking process. I never know whether I should copy large book paragraphs into my notes or whether I should summarize them. I have little knowledge about how to make the most value out of my note taking process. Is there any good book recommendation or resource to help me answer these kind of questions ?
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.