note: this method is recommended for when you have each color of marking on its own layer. it can work for other coloring styles but may require personal adjustments.
click images for bigger pics.
1. color the pet to your heart's content. ignore shading and highlight layers for now.
2. color the shading layer (usually set to multiply at 60%) the same color as your base layer. if your base layer is very light or dark (or yellow or orange), you may need to make a slight adjustment to the color so that the shading is visible and does not appear muddy. highlights should be maintained as white (usually on overlay at 100%) unless you employ a different coloring method for highlights.
3. use the Quick Selection tool on the Base layer to select the full area of the pet that is flat-colored. a dashed line will appear around the area of selection. ensure that no body parts are missing from the outline. [the area selected will only include colored pixels on the layer you are on; in the example below, the feather crest is in a different folder.]
4. while your selection is active, select the shading layer, and add a new layer mask. this will create a mask on the shading layer that shows only the areas selected (e.g., the area of the base layer). tip: if your layer mask appears to be the opposite (black inside + white outside), hit ctrl+i while on the mask to invert it. you want the area of the pet to be white so the shading will show within the lines.
5. right-click the layer mask and pick "add mask to selection". Another dashed line showing the bounds of the mask (outlining the pet) will appear. Move to the highlight layer, and create a new layer mask. The same thing as in step 3 will happen; a layer mask with the bounds of the base layer will prevent the highlights from going beyond the edges of the base layer. The reason for doing this on the highlight and shading layers is so that they can be unclipped from the base without creating a million artifacts for you to erase. This will allow you to clip the markings to the shading in the next steps, effectively auto-coloring your shading.
6. shift-click all your marking layers to select them. then, right-click them and duplicate the layers. note: duplicating the layers will unclip the layers above them. this is okay for the shading and highlight layers, but you may need to re-clip other layers once you move the ones you have duplicated.
7. move the duplicated layers between the shading and highlight layers, then clip them to the shading layer. once they are clipped, your shading will match the pet! please note that, again, for light or dark marking colors (or orange or yellow), you may need to slightly adjust the color of the layer so that it is visible and not muddy.
there are a few ways to color lines: (first - make sure they aren't on Multiply!!)
option 1: semi-manually color them.
step 1: duplicate your marking layers again and drag them up to the line layer. clip them to the line layer.
step 2: choose appropriate line colors for each marking color and the base color. then, color over each layer accordingly.
step 3: do any clean up and color the eyelines black & the iris appropriately. (note: I should have gone slightly darker on these lines! my tablet made them look more contrasty than they appear on most other screens. -_- )
option 2: darken them with an adjustment layer & then clean them up. this method may not work super amazingly on aaaall colors, but it's also not hard to test if you want to try it out.
step 1: add a solid color-filled layer clipped to the lines in the same color as the base.
step 2: duplicate marking layers and clip them to the lines above the color-filled layer.
step 3: create a hue-saturation adjustment layer, clip it to the lines, and adjust until things look alright.
step 4: clean up the lines, color the eyelines black & the iris appropriately. you may need to tweak some line colors during this stage if the adjustment layer didn't work nicely for all of them.
