Regarding the mobo PWR_FAN connector, it has only one possible use. IF the wires coming out of the PSU also include one set with a fan connector on the end, plug that into the PWR_FAN connector. All it does is send the PSU fan's speed signal to the mobo. But if you don't have such a connector (many PSU's do not), just leave that unused.
The two CHA_FANx mobo connectors can be controlled by the BIOS of the mobo. At least one can be controlled by reference to a temperature measurement sensor built into the mobo. The other may also be controlled that way, or MAY be controlled only in the sense that you can set its fixed speed in the BIOS Setup screens. Even a connector that CAN be controlled according to measured temperature usually also has the option of manually setting a fixed speed in the BIOS. That is probably your best option for the RAM cooler, because I doubt there actually is any temperature measurement signal available in the RAM modules themselves. So you could connect the RAM cooler to one of those mobo pinouts and set its speed in BIOS according to your own observations of RAM temperature.
For the 6 case fans that all have Molex connectors, you probably need 3 or 4 of the adapters that convert one Molex output from the PSU into two. Using them you could convert two outputs (or three) to six and feed all your fans. Now, you also have the NZXT fan controller, and you could use those adapters on its outputs to create enough connectors to feed all the fans that you want to run from it at reduced speeds. Any you want to run full speed all the time can just be connected directly to the PSU's output.