When uploading a file, link, or Dropbox / Google drive document, you can set permissions using the icon on the far right of the input field.
The users you check when uploading the file will have access to the document, however, the Project Managers on the project and all Admins will automatically have access to the files. No one else will be able to see or open the file you have uploaded.
Once you've uploaded the files, you can change the permissions at anytime in the sidebar. To do this, click on the file row and then click the + button to the right of Permissions. You will get the drop down menu with all users on the project. Once you make your changes, simply click Done to save them.