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.
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.