By design, Asus intends that the Ryujin-II radiator fans be connected to the included fan controller, and that Armory Crate be used to control their speed.
You can, however, plug them into the motherboard if you wish. The CPU header will work, as will any other fan header. You can then use the Bios or another fan control utility to control them.
I have tried it both ways. If I could control the pump without Armory Crate, I would probably ditch Armory Crate and connect the fans to the motherboard. But since I'm stuck with Armory Crate for the Ryujin-II pump (it cannot be connected to a motherboard port), I just connected the radiator fans to the included controller as intended, and use Armory Crate to control both the pump and the fans.
What's really sad is that Armory Crate doesn't have any option to control the radiator fan speed based on coolant temperature. Armory Crate knows the coolant temperature and can display it on the Ryujin-II display, but there is (as yet) no way to use anything other than CPU temp to control the radiator fans.
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Z690-E, i9-12900k, 2x16 DDR5, 980pro nvme x3, Ryujin-II 360, Strix Animate-II, Evga 3090 ftw3