Many people recommend taking all your notes on notecards. The advantage of notecards is that if you write very specific notes, or only one idea on one side of the card, you can then spread them out on a table and rearrange them as you are structuring your paper. They're also small and neat and can help you stay organized.
Some people find notecards too small and frustrating to work with when taking notes, and use a notebook instead. They leave plenty of space between notes and only write on one side of the page. Later, they either cut up their notes and arrange them as they would the cards, or they color code their notes to help them arrange information for sections or paragraphs of their paper.
Notetaking is the process of extracting only the information that answers your research question or supports your working thesis directly. Notes can be in one of three forms: SUMMARY, PARAPHRASE, or DIRECT QUOTATION. (It's a good idea to come up with a system-- you might simply label each card or note "s" "p" or "q"--as a way of keeping track of the kind of notes you took from a source.) Also, a direct quotation reproduces the source's words and punctuation exactly, so you add quotation marks around the sentence(s) to show this. Remember it is essential to record the exact page numbers of the specific notes, since you will need them later for your documentation.
Work carefully to make sure you have recorded the source of your notes, and the basic information you will need when citing your source, to save yourself a great deal of time and frustration--otherwise you will have to make extra trips to the library when writing your final draft.
Grouping your notes should enable you to outline the major sections and then the paragraph of your research paper.