The publication of user manageable AutoCAD Layers (accessed by the ULAYERS command) and DWF Previews are controlled by the Custom Properties of the Autodesk supplied DWF6 eplot.pc3 driver.
Plot to DWF publication can employ either or both plot by Display at 1:1 scale or plot by named View with the appropriate Annotative scale. Different DWF control Frame results are based on the By Display or By View method employed. This difference can be both helpful and/or disconcerting for Civil 3D users new to the technique. The current DWF6 eplot.pc3 driver plot methods do produce differently sized image (and somewhat deceptive) control Frames for the DWF in By View publications.