Whatever system you use for organizing your research notes, it should achieve these three goals:
Which ideas or quotes are attributed to which sources?
What are the boundaries between your ideas and others' ideas and words?
How can you economize? Focus on information at this stage, not formatting issues.
(One efficient way to achieve all three goals is to simplify citation with a citation manager, like Zotero!)
Any system of tracking research notes should have a system for tagging quotes with source information in a way that keeps tags attached to quotes as you re-arrange the order. The word processor method benefits from the speed and ease of copying and pasting. The disadvantage is that re-arranging quotes can be a little slow.
If you prefer to work from printouts of articles and photocopies of book chapters, this technique might work for you, though it is likely more time-consuming than other methods. It also carries the risk of your paper blindly following the organization of the source articles.
If you would rather work on paper, here is a time-tested method using 3x5 cards. Though it might be a little slower to hand write (and later re-type) quotes, the last step of re-arranging cards into an order that makes sense can be much more efficient than the word processor version:
As you research, you will very likely find that you are tempted to start writing in an open doc window while you have multiple tabs open to various articles you have just found in databases. You may also be tempted to skip the steps in methods 1-3 that allow you to digest and re-organize source information, and just copy and paste text directly from source articles into your paper.
Don't do this.
See methods 1-3.
Why? It will satisfy criteria 3 (Speed), but sacrifice 1 (Clear Attribution) and 2 (Clear Boundaries). When you are in a hurry, copying and pasting directly from articles to your paper, you will lose track of the boundaries between your ideas and the source ideas. You will mistake other people's ideas and words for your own, and neglect to cite them. You will also close a tab before noting the source information; then you either have to abandon that great quote, or attempt to find that source again. Or... the third option, use the quotation but fail to cite the source. Which you can't do, because you understand Academic Integrity.
Citation often causes anxiety. Of course it does! Citation style rules are about the worst combination of arbitrary, complicated, and precise, and because they are often mentioned on the same day as plagiarism, they can have a powerful negative emotional charge.
Anxiety about citation can even cause people to avoid using a potentially great source just because they don't know how to go about citing it. In other words, fear of a small consequence (a few docked points on the bibliography) leads them to risk a bigger consequence: less engagement with ideas, less learning, and a less informed and less interesting paper.
You, however, won't make that mistake. You know that as long as you record everything as instructed on Recording Source Information, keep it organized as shown on this page, and learn resources for formatting on the next page, you can use any kind of source imaginable, and it will all work out.