Hidden masks part of your dergon's genotype, making one gene fail to appear on the design. 

Only one gene can be Hidden on a single design; if you choose to hide a mutation, you cannot also hide a marking! Other options for hiding or removing genes are available, but as a free option Hidden can only affect one gene at a time. 

When used, it should be listed under free options as Hidden: Gene with your specific choice listed! This can be either the name of the gene or the code as it appears in the genotype; Hidden: Blanket, Hidden: +cc, and Hidden: MskMsk are good examples!

Hidden can affect one Hue or Value gene. One gene out of Ww, Bb, +c/cc, +m/mm, or +y/yy may be hidden! When hiding Value genes, you cannot go into the Calico range. Either Ww or Bb must still be shown, however, a Stone base may become functionally Chalk or Onyx.
A couple options are available once a gene is hidden; The hidden base gene may affect the entire design, or the base color choice only, letting markings still follow the original color family.
You may also do this with Gemtone or Chroma bases, for example Prismatic with +cmmyy may ignore the het. +c, leaving +mmyy displaying as the Gemtone color Citrine. You can also hide one part of a Gemtone marking, such as making Amethyst (+ccmm) display as Sapphire (+cc).
You cannot hide the entire Vibrant section if more than one hue gene is present; a Green family (+cy) dergon may become Blue (+c) or Yellow (+y), but not fully Natural. However, doing this with only a single Vibrant gene such as Rain (+c) will leave you with a natural base- Stone in this case- and your markings may be Natural as well, instead of having to show at least one color from your original base. 

When hiding a marking, the option is fairly straightforward; Hidden causes it to simply not appear in the design! It remains in the genotype, can be passed on to offspring, and if redesigned, the marking can be added back into the design. 

Any mutation which appears as a gene code in a genotype can be hidden; this includes Body Types, Variations, and Color mutations, as well extending to Mild Strange, Extra, and Missing parts.
Penalty mutations from inbreeding cannot be hidden! If they affect your design, they'll take effect as usual, and stat penalties cannot be hidden.
Some Color mutations can be listed as Carried when the gene is Het.; in this case, it will not appear on the design, so you do not have to use Hidden on it.