Let's break this down.

undyColor and bodyColor are two palettes used in the creation of a species that replace and dictate colors used by replacing colors on the basic texture with new ones. undyColor is used in humans to set, well, the underwear color, while bodyColor is used for skin. undyColor is also used for Hylotl 'belly' color and other such things. While they're used for the same thing, undyColor is basically a copy of bodyColor so that the two can be used independently.

Here is an example of color palette, taken from some stuff I did with the Daim's Dummies mod. It's awful in-game, but it gets the point of what color palettes are across.

  "bodyColor" : [
    { "ffe2c5" : "ffe9d3", "ffc181" : "ffc181", "d39c6c" : "d39c6c", "c7815b" : "b97551" },
    { "ffe2c5" : "fff6f6", "ffc181" : "f7d5d3", "d39c6c" : "d1aaa1", "c7815b" : "a27f70" },
    { "ffe2c5" : "fff7ec", "ffc181" : "f9d3a9", "d39c6c" : "d3a57c", "c7815b" : "b37c5d" },
    { "ffe2c5" : "fbe1d4", "ffc181" : "f6baa2", "d39c6c" : "cc9582", "c7815b" : "ac7261" },
    { "ffe2c5" : "f4e0ba", "ffc181" : "e9b768", "d39c6c" : "c18f54", "c7815b" : "a2683d" },
    { "ffe2c5" : "e8cebc", "ffc181" : "cfa97d", "d39c6c" : "ae774b", "c7815b" : "804e34" },
    { "ffe2c5" : "e1b98d", "ffc181" : "c88959", "d39c6c" : "9e6a4d", "c7815b" : "784930" },
    { "ffe2c5" : "c9b181", "ffc181" : "ac8348", "d39c6c" : "87633f", "c7815b" : "694c31" },
    { "ffe2c5" : "c5ad98", "ffc181" : "a47a59", "d39c6c" : "865d40", "c7815b" : "66412e" },
    { "ffe2c5" : "ab8c77", "ffc181" : "86644a", "d39c6c" : "684431", "c7815b" : "40271d" },
	{ "494949" : "969696", "3f4442" : "8b9692", "2d332e" : "859688" }
  ],
  "undyColor" : [
    { "dc1f00" : "4d76ad", "be1b00" : "395187", "951500" : "20325b" },
    { "dc1f00" : "7c41b8", "be1b00" : "6c2f90", "951500" : "471962" },
    { "dc1f00" : "c63442", "be1b00" : "9b2724", "951500" : "6a1210" },
    { "dc1f00" : "eaa245", "be1b00" : "b47020", "951500" : "834a0c" },
    { "dc1f00" : "e3e13a", "be1b00" : "a8a614", "951500" : "848008" },
    { "dc1f00" : "6ab841", "be1b00" : "45902f", "951500" : "296219" },
    { "dc1f00" : "535353", "be1b00" : "363636", "951500" : "111111" },
    { "dc1f00" : "e6e6e6", "be1b00" : "979797", "951500" : "6f6f6f" },
    { "dc1f00" : "9e9e9e", "be1b00" : "6e6e6e", "951500" : "434343" },
    { "dc1f00" : "f794f8", "be1b00" : "d355c1", "951500" : "b72c95" }

The first collum of a set is the color on the base texture, and the second is the replacement. So, if, say, the skin color was #000000, and I wanted it to be #FF0000, I'd make it { "000000" : "ff0000" }

Now, here's what the base Lyxaris texture appears as: http://puu.sh/8KHK2.jpg Or at least, an approximation of what it appears as. Let's say I wanted the blue set of markings. The skin color is, at least, for main body, #494b48. So, I would make a table that does the following under undyColor (which will act as skin, as skinColor overrides undyColor, which is important.)

{ "fadc08" : "494b48", "f40604" : "494b48", "4dfd16" : "494b48" } So on and so forth. That's obviously not all the colors, but you get the idea- each and every color BEFORE the colon is a marking color, and each and everyone AFTER the colon is the skin color. It will erase all the colorful little lines on the base texture and replace them with skin color. undyColor is overridden by skinColor, meaning that skinColor's palette will always be prioritized. This means that skinColor will ACTUALLY be the marking color, and undyColor will serve as skin. undyColor will replace ALL markings with its own color, but then skinColor's change will be prioritized and will replace a single marking color with... well, its own color, and then some variants. You will have to flip through 6 colors of each of the 5 types of markings, so it'll take a little while to scroll through all of them, but this system is a lot less clunky than anything else we could think of.