Note that for Separation Preview to work you need to have the Transparency Blend Space to be CMYK mode. CMYK 0,0,0,0 is not white but paper colour. If you have Overprint enabled then it is transparent (but it will warn you), note that Overprint is irrelevant in an RGB document. In Separation Preview, you will see additional inks besides CMYK, and you can view then together or separately to analyse your work. I normally place opaque white, above other colours even if it will be printed first. This way it is easy to toggle on and off. Let it be a colour you can distinguish from the white of the "paper". Normally white ink (as spot colour) is created using a Spot colour with a pink or green appearace, so that you can see where it is (since the artbaord is white.) Pantone white is not good white though, but UV printers using a RIP like Onyx use a spot colout called "Ink_White" for mapping to an Opaque White ink.   A spot colour with overprint should not knock out other layers… I do it all the time). This process is also used for Cut, Crease, Embossing, Varnishes and/or Foil where it is also impossible to visuallise correctly. (In Adobe Illustrator the Plugin ESKO Studio is used in many pcakage desugn firms where they need to visualise speciality inks, but it is still possible to design and proof, using experience to evaluate the results.) When one channel only is visible, then you will also see it as a film where the areas of ink are shown in Black, even if the ink in you press will be white.  Please if you share an example of how you are experiencing your work (a close up is fine) with the Separation Preview clearly visible.  Overprinting is a per channel operation so if you have a CMYK image and overprint a low percentage 1% in a Process colour it will limit that Colour to the top %, and it appears knocked out but it isn't, it's the 1%. In some rare cases you will not be able to Overprint but can use the "Darken" blend mode (Even if it is a lighter colour.) Think of Darken as "And also add this colour", so a Varnish, Metalic or white will not actually make the image darker. Avoid using Other bledmodes that use multiplication when mixing Spot colours, Multiply should not be used with Spot Colours. Some Transparency or effects may interfere with spot colours, but Separation Preview should help you trouble shoot.  ... View more