I cannot seem to find any documentation on this but I want Zotfile to rename all of my pdfs that I save in a particular directory in the way that the Mendeley Desktop manager does. Currently I have to rename them by clicking on each file reference through Zotero, and it does not seem to obey the renaming rules I've set in the Zotfile preferences. On the Zotfile website it says that it can automatically rename pdfs. How can I enable this renaming feature?
It's not exactly clear what you want to do
What do you mean by "save in a particular directory"? Are you looking for a "watched folder" functionality (i.e. automatically import PDFs from a particular directory and rename them based on metadata)?
The rest of your question seems to imply that you simply want to rename PDFs that are already imported in Zotero and attached to Zotero items (i.e. have metadata), so I'll answer that part.
After installing ZotFile (as a Firefox add-on if using Zotero for Firefox or as a Zotero Standalone addon otherwise), open ZotFile preferences via the Gear menu. On the Renaming Rules tab, fill out the preferences to your liking. Do not select Use Zotero to Rename. Select the items that have the attachments you want to rename or select the attachments directly, right-click the selection, go to Manage Attachments and click Rename Attachments. The attachments will be renamed.
This will not move the attachments. They will remain in the Zotero "storage" folder (assuming these are not linked attachments). If you want to also move the files to a different folder, you can use ZotFile's "Send to Tablet" functionality, which essentially moves selected attachments to a specified folder. The settings for that can be found in ZotFile Preferences -> Tablet Settings.
Note that changing ZotFile's renaming settings has no effect on Zotero's built in attachment renaming system. This is controlled via the "attachmentRenameFormatString" hidden preference