First thing to recognize is that every AIO system is designed differently. What you have been doing with your old system is NOT what its required for the new one. You should always do what the system you are installing says to do in its manual.
From that manual I can see that CONTROL of the system has two options. These address control of the speeds of both the pump and the rad fans. There is a switch to position on top of the pump by rotating a ring. The basic approach is that the existing CPU_FAN header's control abilities (in the default "Standard" Profile) is quite sufficient. That means that the rad fan speeds are controlled by the CPU_FAN header based on the temperature measured inside the CPU chip by its sensor. It appears that, if you set the top-of-pump switch to "PWM", that is exactly how the CPU cooling is controlled while the pump speed is kept constant (probably at max). However, if you chose the "Auto" option on the pump switch ring, it also uses some temp sensor (probably its own) to decide when it can slow down the pump speed (at low workloads and temps) to reduce noise somewhat. You get to choose whether or not to use that feature.
You ask about continuing to "set fan speed independently in bios". Now, you had your rad fans connected to a mobo "fan header" but we don't know which. Ideally those rad fans would have been under this same type of control guided by the CPU internal temp sensor. But your comment suggests you are accustomed to manually adjusting the fan fan speeds. Although that is not necessary and NOT what is intended with this Fractal Design system, you probably could do that if you choose. The difference is solely that the rad fans are controlled by the CPU_FAN header, so that's where you would go for manual controls. The PUMP speed is not affected by the setting of this header, but it IS altered by the Fractal Design system IF you choose the noise-reducing "Auto" setting on the pump.