Generally speaking, markings can layer however you choose, but they should not obscure other markings.

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Recessive Color Mutations and other color modifier type markings such as Ombre or Luminescent will always "layer" over other markings and change their appearance according to their individual color specifications.

The only markings that cannot be affected by any sort of color modifier is Piebald and Inked.

 

Markings such as Fade, Tarnish, and Mirage will always layer on top of most other markings:

Crystal, Piebald, Inked, Amphi, Delic and Vitiligo are the only markings that will always layer over every other marking and can fully obscure other markings.

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When multiple of the "top layer" markings are present at the same time, they may layer over each other however you choose as long as neither are fully obscuring the other.