I bought a set of DeepCool fans that states that they are Razer Chroma compatible, but when I plug them into my motherboard, they only work with the motherboard's RGB software. What am I doing wrong?

The problem usually comes down to the fact that the motherboard is not Razer Chroma certified. Fans, like the RF120s, are compatible with Razer Chroma, but the motherboard is what is controlling the lighting of the fans. Similarly, you would not be able to use Asus Aura with an MSI motherboard (unless you have an Asus Aura compatible A/RGB controller) for the same reason.