Maintaining references for preparing a manuscript is always a tedious work. I just need to know about the easiest available techniques to maintain my references.
The best way to manage reference as you're preparing a manuscript is through reference managers. There are several free and premium softwares to choose from.
Free Desktop Softwares
1. Mendeley Desktop and Web
2. ACSWorx
3. Zotero
Premium Softwares
1. Reference manager
2. Endnote
I prefer Mendeley because of its more intuitive user experience.
I recommend Mendeley, but I know Zotero is equally well thought-of. And both are free. Don't use Cite This For Me, because you'll lose your references after a week unless you use the paid-for version.