Help connecting the fans please

Best option is to replace the fans. I'm pretty sure they are only 80mm fans. you can get those fairly cheap. The box fans should have adapters for 3 pin to connect to the motherboard and Molex for a direct connect to the PSU.

the 4pin connector on your motherboard is for your CPU Heatsink Fan.

There is no need to replace the fans. You have several options.

The first and easiest option is to connect the case fans to the power supply with the large molex connectors. You can daisy chain them together as the case fans use very very little power compared to the cpu or gpu.

You second option is to purchase an appropriate molex to fan cable adapter and connect the fans to the motherboard fan connectors. The cable adapters are readily available for a few dollars from online vendors. How many you can connect will depend on how many fan connectors your motherboard has. Do not connect a case fan to the motherboard connector for the cpu heatsink fan. That connection is typically marked CPU_Fan or something similar. Your system will monitor the cpu heatsink fan. Your system may or may not monitor the case fans connected to the motherboard.

Isn't freedom of choice great?  

JohnnyLucky is right, you must use the mobo's CPU_FAN connector ONLY for that function. In addition, if your mobo has a connector for PWR_FAN, it can ONLY be used for a special lead/connector coming directly out of the PSU - and some PSU's don't have them, so you can't use this mobo connector at all. Case fans should only be connected to mobo ports with labels like SYS_FAN1, etc., or to spare PSU power connectors.

Or a separate fan controller.