There are pros and cons, but in your case i would recommend you put the Files into the Content tree, as then if you update the file, it will be 'updated' for anyone accessing it.
You can use the media library, but it currently is kind of a pain to replace a file and preserve the same name. If you uploaded the file, it would add a "-1" at the end of the file if it found a duplicate, and thus you would break the links.
Plus on the content tree you can control who has accesses, and even do different languages.
Media library is great for static files that don't change, and is what we primarily use, but in your case this is where you want to use the CMS.File type.