On fan connections and PSU output connectors:
A mobo has typically one CPU_FAN connector, one or two SYS_FANx connectors, sometimes a PWR_FAN connector, sometimes a NB_FAN connector.
The CPU_FAN connector MUST be used only for the CPU Fan (on top of the heatsink). The 3-pin version has 2 pins for power supplied to the fan, and one pin for a signal coming back from the fan to tell the mobo the fan speed. Of the 3 wires going to the fan, black is Ground (0 volts), red is supply (up to 12v) and yellow is speed. Fan speed may be controlled by the BIOS by changing the voltage supplied on the red lead. This voltage control is based on actual temperature measured by a sensor in the CPU and fed to the BIOS by a CPU package pin. The BIOS also monitors the speed signal and can send out an alarm and take other action if the speed signal fails. The newer version of this adds a fourth pin and wire to provide a different type of speed control instead of changing the voltage. The connectors are designed so that a 3-pin one on the end of the fan wires can fit onto a 4-pin socket but not actually use the 4th pin. There is only one way to fit the connectors together so you can't do it wrong. You must NEVER plug a power source into this mobo connector.
The PWR_FAN connector on some boards is only there to allow input from a special set of wires coming from the PSU to give the mobo the speed signal from the fan inside the PSU. The mobo does not control that fan, it only reads its speed and may be set to put out an alarm if it fails. If the PSU does not have any such connector, simply don't connect anything to this mobo pinout.
SYS_FAN1 is where you plug in a case fan. Just like the system for the CPU, this combo gives the mobo a fan speed signal and provides a voltage to the fan that may be varied to achieve control of a temperature sensed somewhere on the mobo, not inside the CPU. It may have 3 or 4 pins on the mobo pinout, and again it will accept 3- or 4-pin fan connectors, only one way. SYS_FAN2 is another case fan connector including a speed signal. It may or may not be controlled according to a temperature measured in the mobo.
NB_FAN is for when you have a dedicated cooling system on the Northbridge chip, similar to (but smaller than) the CPU fan / heatsink. Many current mobo's do NOT have such active cooling systems, but use just heatsinks and heat pipes to cool the Northbridge. If you install an extra cooling fan specifically for that chip, this is where to plug it in; otherwise leave the pinout unused.
A typical peripherals power output line from a PSU will have one or two Molex connectors on it (4 round female contacts in a straight line, typically used for optical drives and IDE hard drives), plus an extension with a smaller female 4-pin connector. That final smaller connector is to supply power to 3½" devices like floppy drives. Do NOT plug this into any mobo connector - it supplies power only to specific devices!
With many fans such as you have, you need to figure out how to provide power to them all. The CPU fan is easy - only one choice. The first two case fans are straightforward - use the mobo SYS_FANx pinouts. For the rest, the simple choice is to use the Molex connectors, but that usually requires adapters that convert Molex to fan 3-pin male connectors. When you do it this way, all fans connected directly to Molex will have full voltage always and run at full speed. If you wish, you can buy and install in these fan supply lines some manually-set fan speed controllers that simply give you a two or three fan speed choices besides full speed. An alternative may be to rig wiring to allow two fans (instead of one) to run in parallel off one mobo SYS_FANx connector, but you must disable one fan's yellow speed line to avoid confusing the mobo speed sensor with two overlapping signals.