There are 3 separate outputs to which 3 fans each can be connected. The 3 fans per group are always controlled in the same way. However, if you only have 3 fans, you can connect them to 3 different outputs and thus assign different colours.
The colour control is done with the mainboard software. I have a Gigabyte board and therefore have to use "RGB-Fusion". Unfortunately, this software is lousy.