@Mr100dragon100
The best way is to follow color theory. If you look at the Mane Six, every one of them follows color theory:

Pinkie Pie and Rarity are monochromatic (Yes, Rarity actually IS a very very VERY pale blue, color code F1F1F3), Twilight Sparkle and Applejack are analogous, Fluttershy is triadic, and Rainbow Dash is,
hilariously enough, square. If you pick colors that compliment each other they’ll look much nicer. I find too, that ponies look better when you lean away from green as a base color. There are exceptions, like Lyra, but generally I find green color schemes to either look toxic or otherworldly :D
Also too, search online for colors and color palettes that already exist and tweak them as necessary. For example, it’s no coincidence that my Akaname and Rokurokubi characters both use traditional colors of Japan, the former uses Fujimurasaki as her coat and Kōbai-iro/Ikkonzome/Sakura-iro for her hair, an analogous color scheme, while the latter uses Sora-iro for her coat and Kachi-iro/Konjō-iro for her mane, a monochromatic color scheme, albeit both have slightly tweaked color schemes. Other than that, the only “special” things about their designs are the Akaname has a draggled mane (to reflect the “filth licker” monster she’s based on) and the Rokurokubi has very almond-shaped eyes, which along with their lack of cutie marks makes them just look a little bit “off” to reflect how they are actually monsters :D