First of all, the fans have two connector types on them, but you must use ONLY ONE for each fan. Do not try to connect both connectors of one fan to power supplies. The Molex connectors should be male (with 4 pins in a row recessed inside a shroud), whereas the 3-pin fan connectors should be female with little holes to fit over pins of a fan port.
The case's built-in fan controller can be used. Most such units have a 4-pin MALE connector on a cable to serve as the power input for the controller and its fans - the matching FEMALE connector is on wires from the PSU. Then the controller has several output connectors for the fans. You indicate that it seems to have both 4-pin Molex (should be female) AND 3-pin (should be male with pins) fan ports. Maybe it has only 3-pin male ports? Anyway, for each fan pick ONE connector type and plug in. You need to understand two important points about such a fan controller. It allows you to set your own fan speeds as you see fit. Most such controllers have NO way to do "automatic" control according to temperatures. This means that YOU are responsible for adjusting the fans manually ans ensuring that cooling is adequate at all times.
Your other option would be to ignore the controller and connect your fans to mobo SYS_FAN ports, allowing the mobo to do its default automatic control of fan speeds. What this does is track the actual temperature measured by a sensor in the mobo and constantly adjust fan speeds to keep that temp under control. BUT you have a significant restriction. Since your fans are of the 3-pin design (meaning they only operate in Voltage Control Mode), you can only control them by a 3-pin SYS-FAN port on the mobo. If your mobo has only 4-pin (PWM Mode) SYS_FAN ports, those ports cannot do the automatic control. Any 3-pin fan plugged into a 4-pin port will only run at full speed.
Now, sometimes fan count does not match port count. You can buy 3-pin fan splitters that turn one mobo SYS_FAN port into two plugs for fans, and most mobo ports can handle two fans but not more.
Of course, you could even set up some combination of mobo auto control of some fans and front-panel controller connections for others.