The first and third posts above actually are two very different systems.
First one. Your case has all its fans under the control of a controller in the case, and all their power comes from the PSU. That controller will allow you to set MANUALLY what speed those case fans run - maybe only using words like "Hi, Med, Lo". There is NO communication between those fans and your mobo, so the mobo does not even know they exist. The mobo cannot tell you anything about them, and can NOT control them at all.
IF you want your case fans under automatic mobo-based control you will have to replace them. But before you do that, post back here exactly what mobo you have. Then we can look up its fan control details and tell you what KIND of fan you need. Post also how many such fans you plan, so we can advise how to connect them.
Third post: you have a Phanteks case that includes their PWM Hub. This Hub requires a PWM signal input from a mobo fan header that actually uses PWM Mode for control, and then it uses that to power and control all the fans plugged into it. To do that, it also requires that you plug a cable into a SATA power output connector from the PSU. It is a unique Hub in one important way. Most such Hubs only share the PWM signal to their fans, and that means they can only control 4-pin fans. But the Phanteks PWM Hub uses the PWM signal from the mobo header to create its own group of 3-pin output ports using Voltage Control Mode, and that system can power and control any mix of both 3-pin and 4-pin fans. The Hub's instructions try to prevent a problem some people have with odd mobo ports. So they tell you you must plug its input connector into the CPU_FAN mobo header, because that one is SURE to provide the PWM signal it needs. That also means that you MUST plug the actual CPU cooling fan into the WHITE Port #1 of the Hub, and other fans in other ports. That Port #1 is the only one that can send its fan's speed signal back to the mobo CPU_FAN header, and it is important for your system's protection that it monitor the CPU cooling fan.