eDocBuilder does not have any way to "split" the output file into two PDFs as you describe. The best that you can do is to define a spot color named UV, and make use of that color for the objects that need UV coating coverage -- either objects in the master PDF or text fields added by eDocBuilder. (Graphics added by eDocBuilder would need to be uploaded as PDFs that also make use of the spot color.) This will then show up as a separation when the PDF is ripped.
Most printers that do process + spot color are perfectly fine with PDFs containing spot color separations.