Within your account, you can set default Reading Options, which will be applied to all new titles when they are created. These default options will automatically be applied when content (PDF or ePub file) is uploaded. You can always change the reading options for an individual title record from the Title Details page (for example, if you usually enable Kindle, but have an image-heavy file that requires the Kindle Download option to be turned off).
To do so, click your Account Settings at the top right of your account. In the side-bar at the left, look for "Defaults for New Titles" and click the arrow next to "Reading Options"
Learn more about all of your file security options here.