If you have a desktop computer, do not waste time transferring all your notes on to it. Use underlining or other emphasis for showing structure, even retrospectively. Main themes - highlight key words, central arguments etc., but do not note repetitions, since these are usually a device for highlighting and structuring. Excerpts - write down verbatim passages in a book which are important, especially if you do not have a personal copy of the book. And be sure to note the page number.
Traditional notes run along the line in rows down the page.
You can make these clearer by numbering points, indenting lines, underlining etc. With practice you may find it useful to take notes in the form of mind-maps. These use the page more boldly and involve drawing connections on the page, and may include graphics. Make a start by turning the page from the usual portrait orientation to landscape , and write one or two main keywords in the middle of the page. Then note subsidiary points at the end of a line leading from the relevant keyword.