The USB connection is for the RGB controller. The fans would then plug into the controller. Power for the controller is likely to be separate, likely a SATA connection or possibly large 4-pin.
Not sure what you mean at the end there. Power is always going to come from the power supply. The concept of a fan controller, or even an RGB capable motherboard, is to send that power in deliberate ways to alter the fan speed and the voltage applied to each color of LED to achieve the desired color. Quite a few ways to do it, but it really comes down to how much you have to spend and what you want the end result to be.
I have no specific recommendation on which controller, it would depend a lot on the fans you want and the type of behavior. If you want software control look at products compatible with something like Aura Sync. Though there are a few major brands out there producing high end controllers with bundled software (NZXT would be a good example). The idea behind them is that the fans, motherboard, GPU, CPU cooler, etc are all on the same standard so they can all be controlled with a single piece of software.
If you just want an RGB controller module there are many out there that use a physical remote, and many that come with included fans. Just google RGB fan controller.