Well done on getting your project, hope you have a good time doing it.
Right, I use Endnote. Basically, when i search on scopus or science direct and find a paper I'm going to read, I download and print the paper. But at the same time I download the citation details too, this goes into Endnote, and whenever I'm writing a document and need to reference that paper, I highlight the paper in Endnote, and in Word click 'insert reference'. This puts the reference in the document as a citation, then as a reference at the end of the document, so saves you a whole load of time.
The good thing about Endnote is you can download styles from the Endnote website, this enables you to automatically reference in the style of the journal you plan to submit to (they all have slightly different styles, just to make our lives harder)