That looks amazing with the greens, yellows, and purples, along with the hints of orange and blue. That'd be one beautiful flower if it was real. How do you know which colors to use in different places?
Well that's the thing about Apophysis. You don't really get to decide where the colors go. Sure, you can shift the color gradient "left" or "right" and affect the color balance in the image, but you may get a color where you want it and another color will change somewhere else in the image where you hadn't intended. Being a mathematical/algorithm driven application, Apophysis is the final decider on what colors go where. There's a lot of luck-of-the-draw involved, but in the end it is the artist who decides what looks best to make the final render.