hey, im also running a hydro aio with rgb fans and a commander pro with more rgb fans. im not sure what your question is to be honest. i can tell you how i did it, maybe it helps.
i bought a non platinum hydro aio, so there were no RGB fans in the original package.
i replaced the ML non rgb fans with ll120 rgb fans.
i connected the PWM cables of the 3 fans for the radiator with the 3 Fan Headers that are connected to the Pump/Block.
then i connected the 3 RGB cables from the radiator fans with a Corsair RGB fan hub.
there are 6 slots on each rgb fan hub, and they run in sequence, so it is easy to set up your prefered order by plugging them in accordingly.
then i connected the rgb cables of 3 other corsair rgb fans of the same type (ll120 or ll140) in the same RGB fan hub, and their PWM Cables to the fan slots on the commander pro.
As far as i know, you just put the cable for the cpu fan connector in the mainboard cpu fan header, so that the rpm of the pump can be read out and you get a warning via windows/bios if it should fail.
also, this thread helped me a lot understanding the whole corsair setup:
https://forum.corsair.com/v3/showthread.php?t=173880