What is the best way to archive all references in phd?
Absolutely begin using a reference management software.  If you're planning on writing in LaTeX (which you will if you're in many sciences and engineering fields), something that manages Bibtex files is essential.  I tried several more sophisticated programs like Papers (which is made to work like iTunes) and Mendeley, but I now use a very simple program called Jabref.  Now when I get a new paper, I go to Google scholar, copy-paste their Bibtex entry (they have one for pretty much every published paper) into my master Bibtex file.  Then when I'm working a separate project, I start a smaller Bibtex and copy references over when needed.  Personally, I didn't like programs that tried to offer an "all-in-one" experience with built-in PDF reader, file management, etc.  

My other tip is to name your files in a logical manner to make local search easier.  I use "First few words of title First Author Year"  E.g. "Stochastic Relaxation Gibbs Distributions Geman 1984"