As mentioned before, yes, use a Rich Black and apply it to your Black layer in InDesign (I use 40C 30C 30Y 100K myself : lol). The problem with this approach is it's still a dead-fit registration, so any misalignment could show the lighter undercolour, but it certainly won't be as bad as a white knockout. As said, you don't NEED to make this layer overprint though . If you DO (using multiply), you'll still have variations of colour underneath). This is what I do: First of all, I leave the Outline as a layer in the Photoshop file (I stay at a 600 dpi resolution so the loss of crispness is minimal) with that layer set to overprint (Multiply). To deal with the large black areas, I magic-wand-select all the black in that layer, then Contract the selection 3 or 4 pixels. This may remove any selections that are thin, which is fine, since it's the bigger black areas you are most worried about. Then, on a new layer beneath the Outline layer, fill that with 40C 30M 30Y. Result: 3 layers: bottom layer is your Colour layer, middle layer is the "trapped" Rich fill (40C30M30Y), top layer is the Outline black, set to multiply. I suppose you could technically stay with your work flow, delete the Outline layer from the PS stack, and save your colour part from the remaining two, then add back the outlibne line art file like you do, still setting that to Multiply in ID, but you are setting yourself up for major registration misalignment, and an extra step, so why bother.
... View more