When you create a PDF or DWF from a DWG file, you have the option of including layer information. If you do, then you can turn individual layers on and off in your PDF or DWF viewer.
But did you know that you can also turn on and off layers when you use that PDF or DWF file as an underlay in another drawing? The underlay contextual ribbon tabs put that option right in front of you when you select a PDF or DWF underlay:
Even if you don't have a reference selected, you can find the Underlay Layers option on the Reference panel of the Insert tab.
However you get there, once you open the Edit Layers dialog, there are a few things you can do. You can turn layers on or off (although you can't change any other properties), you can search for particular layer names, and you can switch to a different underlay to control its layers instead. Like many other dialogs, SHIFT and CTRL work to select multiple layers or ranges of layers.