Great questions about including downloadable files in your WordPress site. While you could separately upload these files and link to them, or even insert files in Pages or Posts using insert Media (when creating or editing Pages or Posts) I would recommend using a plugin since you additionally want to be able to password protect some of the files.
While looking into this for you, I found two plugins that offer all of the functionality you are looking for and even help you track the number of downloads of your files:
WordPress Download Manager
WordPress Download Monitor
Both of these plugins use shortcodes so that you can easily insert links to the files you want to make available to your users. Shortcodes are a quick way to add functionality to WordPress. They are one word keywords enclosed in [square brackets] that can easily be added to Pages or Posts.
Please let us know if you have any additional questions or need further assistance.
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