When it comes to organizing your documents, keep it simple.
- Make sure to rename downloaded articles, book chapters, etc. 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.
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.