depending on what you want to do will dictate what you should do. the one fan that HAS to be connected to the motherboard is the CPU cooler fan, no matter what. The other spots on the motherboard are to allow you to connect case fans and usually have the motherboard control the speed. The main reason to get a Fan speed controller is to slow down fan speeds for better air flow and less noise. Yes some have the ability to connect 4 fans but depending on their locations you may need to get fan cable extensions for then to reach the controller.
yes if you put in a controller you will gain an extra 4 places that are controllable for fans. Now if you don't need the control you can buy the 4 pin molex to 3-4 pin fan header adapter and power them off the PSU. Some fans even come with this adapter included. These are your options and the reason to buy a Fan controller.