You have a few options:
1. You can connect the CPU fan to the cpu fan header, connect one of the case fans to the system fan header and connect the other two case fans directly to the PSU using fan to 4-pin molex connectors. The two fans connected to the motherboard headers will have their speed controlled by the motherboard, the two connected directly to the PSU will run on full speed at all times.
2. You can buy a 2-way fan splitter cable and connect two of the case fans to the system fan header with the remaining case fan connected to the PSU. I have seen 3-way fan splitters, but don't endorse their use. I recommend driving only two fans max from any motherboard header.
3. You can buy a fan controller that will allow you to...