NZXT Phantom 410 4-Pin/3-Pin Fan

I believe that case has a controller for adjusting the speed of the fans the case comes with.
What you are seeing are the male connectors that the fans plug into. The cables coming from the fans themselves will plug into those male connectors.

The case's Molex connector plugs into your power supply's Molex connector to feed the fan controller. The fans are not intended to connect to the headers on the MB.

I also have this case and clutchc is right. There is a fan controller for three fans already on the case, those connectors will connect to the controller and then the controller will connect via molex if I remember correctly.

I've solved the problem but I can get the fan controller working.
There are two molex connectors that come with the fan, one with 4 pins and one with 4 plugs.
I've plugged the 4-plug molex connector into my non-modular power supply and it doesn't seem to be working.

The male Molex 4-pin connector from the fan controller plugs into any 4-pin Molex female connector from the PSU. The fan 3-pin male connectors plug into the mating 3-pin female connectors from the fan controller. Your slider control on top of the case will then control the speed of the fans. If you've done as I've directed, and it still doesn't work, the only reason would be a bad controller switch or all 3 fans are bad.