Emboss print-ready files should be supplied as separations. Before you create a press-ready file for your design, be sure to carefully read through Design Considerations for Embossing.
This means the emboss layer is supplied in a separate file (or separate page) of your press-ready PDF file.
3D Emboss
For 3D embossing you will also need to provide a text file (exported as a PDF file) including a description of how you would like the 3D elements produced.
See: Example of a File for 3D Embossing.