Make sure your layers are setup with your template locked as the top layer, foil/spot layers each on their own layer (if applicable), and then the remaining artwork (cmyk) layer on the bottom. Delete any unused layers.
Step 2
Separate your artwork onto each layer accordingly. If you have a logo that you want to print in color and have a clear uv, then you would place the logo on your artwork layer, copy & paste in-place onto your spot uv layer. On your spot uv layer, make your logo a solid shape and a color (like black or magenta for example).
Step 3
Save for print. Always outline your text and embed any linked images. Then you can turn the visibility off for all layers – turning back on only one layer at a time (keep template layer turned on always). With your spot uv layer turned on, save as a print quality PDF. Then go back, turn off that layer’s visibility, and turn on your next layer, save as, etc.
Each time you save a layer, you should label the file name with the name layer name at the end.