In the software, under the LED section, find the "Custom" LED Mode. From there you select a color on the right side using the various sliders available. Once you find the color you want you click the keys you want to turn that color. Change the color again on the right side then click the keys you want to be that color. Rinse and repeat. I use this for a few profiles and have lots of different colors in use on each one.
Take note of the specific colors you're using though (like note down the RGB values in notepad or something) because in my experience it won't tell you what the RGB value of an existing key is so if you want them to be EXACTLY the same you'll want something to refer back to. That's my biggest issue with this software.