I'm not sure what you mean by "I have connected the PWM 4 pin cable to the cpu_fan slot in the motherboard." I note that this case comes with the Phanteks PWM Fan Hub. Maybe you mean that the 4-pin fan cable from this Hub has been plugged into your mobo's CPU_FAN port.
You have not specified which mobo completely, so I'm going to use the manual for the ASUS Maximus VIII Hero model. (I've added notes for the ASUS Maximus Extreme model.)
The PWM Hub in the case is designed to do this: it takes the PWM signal from one mobo fan port and it takes power from a PSU SATA power supply connector, and it uses those to create six 3-pin fan ports for you to connect fans to. This hub is unusual in this: it does not simply create many 4-pin (PWM Mode) ports. It creates 3-pin (Voltage Control Mode) ports from the PWM signal. Now, 4-pin fans can actually run under Voltage Control Mode (and they CAN plug into a 3-pin port) so in this way the Hub provides control of BOTH 3-pin and 4-pin fans plugged into it. Its best use is to use one mobo CHA_FAN port to control all your case ventilation fans IF you don't want to use the individual mobo CHA_FAN ports OR IF your mobo does not have enough of those fan ports for all your fans. So let's go through the setup.
First, the CPU cooler system. I am not clear what you mean by saying "the cpu cooler in top of the motherboard". Do you have a CPU cooler system that is a finned heatsink and fan mounted on the CPU? Or, do you have a liquid-cooling system with a pump on the CPU and tubing running to a separate radiator mounted in the top of the case, with its own fans there? In either case, your best choice is to have the mobo perform automatic control of the CPU cooling by connecting the cooler system to the CPU_FAN mobo port. This system uses a temperature sensor built into the CPU chip by its maker, and changes the CPU cooler system speed to keep the chip's internal temperature under control. To configure this system, see the mobo manual Section 3.7 on p. 3-38 (Extreme model on p. 3-36). The CPU Q-Fan Control can be left on the default Auto setting, or changed to PWM Mode if you are using a 4-pin cooling fan or PWM cooling system. Leave the CPU Fan Profile at the default Standard setting to allow it to do automatic control. If you have a liquid cooling system, follow its maker's installation instructions. I expect they will require that you connect something to the CPU_FAN port and configure it for automatic control as above.
Now to case ventilation. You have a decision. Your mobo has four CHA_FAN ports and each can be configured for automatic control of either 4-pin (PWM Mode) fans or 3-pin (Voltage Control Mode) fans. Now, your case came with 2 fans Pin counts unknown). Even if you install one or two more, you have enough mobo fan ports to control them all WITHOUT using the PWM Hub that came with your case. So, let's cover that situation first: you will ignore the Hub and just use mobo CHA_FAN ports for each fan. Plug each case fan into one mobo CHA_FAN port. (Do NOT use the special Extension Fan mobo port.) For each port you use, configure them according to manual pages 3-39 and 3-40 (extreme model p. 3-37 and 3-38). Under Chassis Fan 1-4 Q-Fan Control, you can Disable any mobo CHA_FAN port you are NOT using. For ones you use, set this according to the fan wiring: set to DC Mode if you have a 3-pin fan, or to PWM Mode for a 4-pin fan.Under Chassis Fan 1-4 Q-Fan Source, your best choice is usually Motherboard. (This item chooses which sensor to use to measure the actual temperature of what you are trying to cool with this fan, so the general built-in Motherboard sensor is usually best for case cooling.) The next few items probably should be left in their default settings for now. Ensure the Chassis Fan 1-4 Profile is set to Standard to allow automatic control. If you connect your fans this way, each of them will be separately controlled by its respective port (although likely they will all run at very similar speeds) and each fan's speed will be available for you to see in the fan control screens.
Alternative situation is if you decide to use the PWM Hub that came with the case and control all your case ventilation fans through it, using the PWM signal from only ONE of the mob's CHA_FAN ports. The case manual suggests that the Hub 4-pin cable be plugged into the mobo's CPU_FAN 4-pin port. This is a precaution because, as they point out in the fine details, some mobos have 4-pin CHA_FAN ports but do not actually do proper PWM Mode control. In those cases the Hub cannot get a PWM signal to use. But your mobo does do this properly (in fact, you will set it that way) on its CHA_FAN ports, so you should NOT plug the Hub into the CPU_FAN port - leave that port solely for the CPU cooling system. Plug the 4-pin connector from the Hub into one of the mobo's CHA_FAN ports. Plug the hub's power input connector into a SATA Power output connector directly from the PSU. Plug your case ventilation fans into the Hub, making sure that one is plugged into Hub Port #1 (with a different color). Now go into the BIOS Setup system for Section 3.7 fan configuration on p. 3-39 (as above) (Extreme model p. 3-37) and make sure the one port you have plugged the Hub into is set this way: Q-Fan Control on PWM Mode, Q-Fan Source on Motherboard, Chassis Fan Profile on Standard. If you connect your case ventilation fans this way, all of them will run at very similar speeds but you will only be able to see the speed of the one that is plugged into Hub Port #1.