If you want to survive your Ph.D. journey, you MUST adhere to some sort of organizational system. Your best bet is to use a reference manager such as Mendeley, EndNote, Zotero, Papers, etc. There are a lot of options out there- just choose something!
Most of these allow you to keep track of citations (books, articles, reports, websites), organize those citations, save and mark-up PDFs, work in groups, and to create in-text citations and reference lists. Sounds magical, right?
The ISU Library primarily supports Zotero and Mendeley. Look through these and other options before making your final choice.