When you add new content to a section it defaults to the bottom of the section. You can move it to a new location within the section it was created in or move it to a new section.
You can also move content using module index.
You may wish to consider disabling the alternative format for a specific file if:
When students select the alternative format icon to download the content in a different format they will receive a message that The alternative formats for this file have been disabled.
You can re-enable alternative formats if required.