You can turn layers on and off in an underlay.
By default, all visible layers of an underlay are turned on when you attach the file. It is usually convenient to turn off any unneeded layers to reduce the visual complexity of your work.
Use the PDFLAYERS or ULAYERS command, Underlay Layers button on the PDF Underlay visor or right-click a selected underlay and click View PDF Layers.
You can use the Properties Inspector to determine whether any layers are turned off in an underlay.