There is no easy way to associate a file with a collection, you’ll need your own system for doing that.
In particular, the way files are stored in the Omeka database requires a connection to an item, and doesn’t allow one to a collection. A plugin can still attach files to collections with its own database set up, but you’ll be rolling your own implementation, more or less.
Not sure if this meets your needs but there is a plug-in Shortcode Anyfile that allows you to insert an image file from an item or your theme’s image directory anywhere you can add a shortcode.