There is no one way to be organized, but there is a way that will work best for you. You could use note cards, outlines, notebooks, spreadsheets, color coordinated file folder, or citation managers. Find your system and then use it.
EndNote X9 - the most recent version that has been licensed by UAB. You can get started by checking out this research guide on EndNote.
"Research" accounts - almost every database gives you the option of creating an account. For more information click here.
Zotero - a free tool that many researchers swear by. Reportedly, the plug-in for the browser works really well.
Notebook - research shows we remember more when we write it down. (Thank goodness because my handwriting is atrocious.)
As you do research, keep track of your sources, and organize them into groups. You might group them based on common methods, research question or findings.
Note: All of these details could inform future searching and save you from having to comb through an article trying to find a lost piece of information!