How to connect case fans mobo pins or PSU power?

You need to check the wiring diagram for a typical 3-pin case fan:

http://www.allpinouts.org/index.php/Motherboard_%28CPU%...

Ignore the first photo, but note the color and functions in the table, and the diagrams below that under Notes. On your case fans with 4-pin Molex connectors, they use the same color conventions - black is Ground, red is the +12 VDC supply. I fully expect there is NO Yellow wire coming out of the fans. This means that, once you connect your fans to your mobo's SYS_FANx pinouts, you will NOT be able to see a fan speed because those fans don't send out a speed signal.

So you'll be doing some re-connecting and soldering to put 3-pin connectors on the end of the wires. Black goes to one end - be sure of the correct end according to the diagrams - and red goes to the middle point in the connector. Now, since you're doing that job anyway, you can connect TWO case fan's leads into ONE 3-pin connector. Just put blacks together, and reds together, so they are in parallel. Most mobo fan pinouts can handle the load of 2 fans, but maybe not three for start-up heavy current. Do this and you can connect four case fans to two mobo SYS_FANx pinouts.

Within the BIOS Setup screens you can then have it automatically control fan speeds, noting that two fans will do the same thing, and the other two something a little different, maybe. IF you have an option on the SYS_FAN speeds in BIOS, set it to "Ignore" so the BIOS won't try to use non-existent speed signals. The BIOS does NOT need fan speed signals to control them - it uses its own temperature sensor for that.

Regarding the CPU fan, just plug it in. The connectors are set up so that they only fit one way, and 4-pin and 3-pin fan ports have the SAME signals on the first 3 pins. From there, however, there are three possible ways the CPU fan speed control could go:
1. If the mobo just behaves always as if the fan connected is 4-pin, your CPU fan will always run at full speed because the red line will always get 12 VDC.
2. If you BIOS allows you to specify the type of fan you have plugged into the CPU
_FAN port, set it to 3-pin. Then it will vary the voltage on the red line to control speed.
3. Some mobos may automatically figure this out without your making any BIOS settings, and feed the fan as a 3-pin with varying voltage on the red line.

I know that the CPU fan connection on the board is supposed to let me know if anything is wrong with the CPU, right? so then if I don't fit into the last pin on the cpu connection, then will my board and cpu still be ok?

And I won't be able to control anything if I plug into the 4 pin peripheral plug on the power supply right? so is that recommended that my fans aren't connected to the board or can just do that since I don't have enough plugs on my board?

With your 3-pin CPU cooler fan plugged into the mobo's 4-pin port, the fan speed signal IS being sent back to the mobo. All mobo BIOS's can display that speed for you and make it available for other utilities to display, also. It is not actually USED in controlling the CPU fan speed. That is based on a temperature sensor built into the CPU itself and monitored by the BIOS. The CPU temperature signal is always there, independent of what you do with your fan. With it the BIOS does at least two things. One is to base the automatic fan speed control on the actual measured temperature - that's a common feedback control loop. The unknown for me is whether it will do that. A 3-pin fan system accomplishes this by reducing the voltage supplied to the fan on the red line when the fan needs to slow down. A 4-pin fan system, on the other hand, leaves that voltage at max all the time and changes another signal on the 4th pin that won't be connected to your 3-pin fan. So, if the mobo acts only as if it is controlling a 4-pin fan, the result will be simply that the fan runs full speed all the time and cools the CPU a little too well - hardly a problem! The second function is to take stronger action of the cooling is insufficient. If the actual measured temperature inside the CPU case rises to a certain alarm point the BIOS slows the CPU operation down a LOT to reduce its heat generation and protect it from overheating. If that in not good enough and the temp rises to a higher alarm point, the BIOS will just abruptly shut down the whole machine to protect the CPU. In some BIOS's there is a third function based on the CPU cooling fan's speed signal, not the internal CPU temperature. If the BIOS senses that the fan is NOT turning (either because it really is not, or because the wiring is failing to deliver the signal to the BIOS), it will not wait for the temperature to rise too high too fast. It will just shut down the machine right away in anticipation that the CPU temp can get disastrously high VERY quickly if the fan is not working at all. Your mobo BIOS may or may not have this third function. Either way, your fan DOES send its speed signal to the mobo via the Yellow lead on it, so all the normal CPU protections will work.

Any case fan connected directly to the PSU output will work at full speed all the time, unless you also install some third-part fan speed controller. The only downsides to not running at lower speeds are: (a) you use a small bit more power; and, (b) they make more noise.The simplest way to get case fans under automatic speed control is to power them from the mobo's SYS_FANx pinouts, but it is common to have no more than 2 of those, and you have 4 fans. You could modify the connectors on 2 fans to plug into the mobo and control only those 2, leaving the other 2 at full speed plugged into PSU outputs. Or, as I said, you could connect two fans in parallel to each of your two mobo pinouts and have pairs of fans controlled by those. Your choice.