MemberGate includes a protected download library.
If you wish to protect files such as pdfs, excel spreadsheets or other files then they should be loaded into the download library.
In your control panel on the lower left is the download library section.
From there you can add/edit downloadable files. Any files can be included such as PDFs, .doc, .xls etc. MemberGate protects these files from being downloaded unless you are logged in as a member of the site.
It's important to note that simply uploading a file to the /members folder of your site does not protect it from download. In order to be protected it must be put into the download section of your site.
Once it is has been put into the download library, you can then click on the listing for that item.
You can copy that URL and include it elsewhere on the site to refer to that document. It will not be accessible unless someone is logged in.
If you do wish to upload a file for the public, you can use the file upload feature found in the utilities section of your site. Putting a file in using that function will make it accessible to anyone without logging in.