Reference management is the act of organising references and generating reference lists or bibliographies in a variety of styles e.g. for a thesis, or for journal or book publishing. Many researchers now use software to do this – this can store both the reference and the PDF of the paper you are reading. Edinburgh Napier offers training & support with Endnote and Mendeley reference management software - use the one which suits your needs best, or choose another reference manager.
Look at the reference management software your university supports, the word processors they link with, and which referencing guidelines you should use.