(Hey Cider - if you see this, feel free to message me. I deleted your post because a lot of the info was off or outdated. Don't feel bad, I was figuring this all out as I went along and have only gotten some of it worked out just recently! Feel free to message me for details).

FIRST THING is,

Don't make either "Color 1" or "Color 2" a pure black or blazing white. It will obliterate all texture detail and you'll make the already-wonky Kenshi graphics look like a Super Nintendo; it'll just turn it all to mud (or a blank white space).

The colors you pick in the mod editor won't look quite the same in-game. Generally, everything will be somewhat lighter and more saturated than that tiny square in the Mod tool. To get a realistic black, use a very dark grey; for white, use a very light grey. Same for colors: make the color in the mod editor a fair bit darker than you really want it to be. In game it will show up much brighter.

Really experimenting is the only way, since everyone's gonna like a different look.

For using the mod editor to alter the existing NPC FACTIONS in game:

Don't bother looking at the "Colour Schemes" for anything other than NamelessPlayer, many of the names are arbitrary and some are entirely unused! Rather, look at the FACTIONS entries, and see if they have a "colour scheme" property already defined, and there you go. I found that some (like the Tech Hunters) did not, so I gave them one. Stuff like that.