When it comes to organizing your documents, keep it simple. Make sure to rename files downloaded from our databases or the internet. The default filenames are often unhelpful, like "contentserver.pdf" or "019967432.pdf". Rename PDFs using the first author's last name and a short title (lastname_shorttitle.pdf). Keep them in the same folder on your computer or citation manager. (Sub-folders are also a good idea, but make sure all your research can be found under the same main folder.)
If I downloaded this article,
Older, C. E., Diesel, A., Patterson, A. P., Meason-Smith, C., Johnson, T. J., Mansell, J., & ... Rodrigues Hoffmann, A. (2017). The feline skin microbiota: The bacteria inhabiting the skin of healthy and allergic cats. Plos ONE, 12(6), 1-18. doi:10.1371/journal.pone.0178555
I would rename it older_felineskinmicrobiota.pdf.