If you are writing a thesis, then presumably you have at least dozens, and probably hundreds, of references. If so, then my strong advice is to install a reference manager. The easiest to use (well, of the ones I am familiar with) is Papers, the most powerful is EndNote. There are others, Mendeley, Bibtex, Zotero being the most well known (and, I think, all three are free), but I am no longer familiar enough with them to comment in detail.
The first thing is to check if your university/college has a site licence for a reference manager. If so, you may be eligible for a free, or substantially cheaper, copy. One of the reasons I use EndNote, apart from it’s massive flexibility, is that my university has a licence for all staff and students. Free and powerful is a good combination for software.
Papers does cost, but their student discount is substantial and, although US $50 can seem a lot as a student, it more than pays for itself in a very short time. I actually used it in addition to EndNote because it was so much easier. Unless you use an obscure referencing system or need to tweak power setting, Papers can now do most of what EndNote can. Note that both Papers and EndNote will work with Scrivener (and Word, and Pages): I believe that both Zotero and Mendeley struggle with Scrivener, although I don’t have first hand knowledge.
The benefit of a dedicated reference and citation app is that you insert the citation, it does the formatting when you are done (preferably after you have compiled to Word). I forget how many hundreds of references I used in my thesis, but preparing the reference list only took a few minutes at the end. And yes, I wrote in APA style.
Papers would be my first choice, I enjoy using it. EndNote is good for power users who like to tinker.
Confession: I was a power user and tweaked EndNote’s settings to correct some minor inaccuracies in the way it presented some obscure types of references. If you are into that sort of thing, EndNote is the one, but if you are happy with the out-of-the-box settings (most people are) then Papers is much easier to learn and use. I have no hesitation in recommending Papers.
Finally, if you really want to manually manage all of your references through all the drafts of your thesis, then… …I can’t help much. Just thinking about it gives me a headache and makes my hands shake.