What are best practices to storing uploads in WordPress?

If you have a lot of uploads, using the /year/month/day/ approach is recommended in order to keep the number of files in each directory manageable. (Just today I ran into an issue where there were more files in the uploads folder [~12,000] than the FTP server was configured to include in a directory listing [~10,000]. This caused quite a headache.)

If the PDF you’re changing periodically is attached to a page or post, upload the new version while editing that same page or post. WP will put the uploaded image into the /year/month/day/ corresponding to the page/post it’s attached to initially.

Edit: there may also be one or more plugins available that allow you to change the path of uploaded media. You could use this if the PDF isn’t attached to a specific page/post to change the path/URL to match the original after uploading.