rename PDF document in stored folder not only within endnote

To annotate my documents I need to access the pdf without going through Endnote and the current storage system of having every paper named unrecognisably in it’s own folder named after a number makes it a real pain to find the paper I need. I use the automatic rename function for pdf’s and it works fab within endnote, it would be nice to be able to choose to rename the full pdf that way (in the storage folder - either in the data folder or in the imported folder linked to endnote).