As far as getting it out of the database in a transformation, you would have to use a custom macro method.
You can get the files stored in the field any way you want by following the example herehttp://www.kenticosolutions.com/Developer-Tips/Tip/May-2011/Many-to-Many-relationships-in-the-Kentico-CMS-Cont.aspx
or by accessing the property and splitting the value in a string array to iterate through and query the document tree.
You can make a custom macro method that takes the field's values as an argument and returns a TreeNodeDataSet that you can apply text transformations to or something.
In short, there are a lot of ways you can use the data stored. It's up to you.
In all honesty, I think the devs at Kentico need to create a form control that utilizes the Document Relationships feature in a controlled manner where we can specify the settings for the control to assign a specific relationship name and set it as the left or right document. If I have the time, I will try to cobble a proof of concept together for that as well. I do think that I will have trouble with it though because there is no way to order the documents in the relationship as far as I know.