Upload directory in Membership plugin

I am using protected content on the site. Right now I am obfuscating both the directory path and the filename. Everything is working well (at last - see my other post on the fix to the multisite 404 error).

However, the obfuscated file path is pretty easy to figure out, since both my images AND my file uploads end up in the same media folder. I don't want to protect most of my site graphics, just the file uploads (primarily PDF files). Is there a way to put the files (PDFs) in a different directory to further protect them? If so, would the membership plugin know how to handle this change?