The motherboard has pins for USB4 connection. The connector that connects to these pins has individual parts which are labelled: (power+, power-, +3 volt? etc). Which of these connectors goes to which pin on the motherboard.
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Here is the link to the Gigabyte site to your specific motherboard. The only place that will have those pin locations is the user manual. Not all motherboards support all chassis designs and at times modification of the connectors is required in order to get the connections. Check the User manual for the actual pin outs.
In the motherboard of any models, there are only two ro four onboard fix ports. Another ports is not the part of Motherboard, there are only free ports pin on motherboards. your cabinet ports connect with there open pin ports.,
Connect the USB header to the USB pins on the motherboard.Generally the connection on the motherboard has 2 rows of pins, 5 on top, four underneath.There are 2 types of headers, 1 rectangular with 5 hols on top row and 4 on bottom. Connect to MB ensuring the holes match up to the pins. You may also have a 4 + 4 connector with 2 grounds. Connect so that the pins match up to the labels on the pins on the motherboard.ie. power, d-, d+, ground.
There are other motherboard USB configurations, but the above is for 99% of them.
In regards to connecting the USB wires this is common because not all case/USB connectors use the same pin connection. What you will need to do is look up the info in your motherboard manual to see where the pins go. Note the wires/connectors should be labeled as well.
Diagonally opposite(diagonally opposite corner) to where you connect your mouse and keyboard, there will be pins on the motherboard to connect the front panel connectors. You can identify it by names written near it like SPK or Speaker, on/off and so on. The connectors on the front panel will also have names written on them. Just match and connect them. Reset switch, Power and speaker will not be a problem connecting. But hard disk light connector will be a little tricky. you have to connect to the correct polarity. USB connectors will be near these pins and will be labled as USB5 or USB4 and so on, on the motherboard. You will be able to insert the USB connector in one direction, so connecting it is not a problem.
Diagonally opposite to where you connect your mouse and keyboard, there will be pins for connecting front panel connectors. You can identify them by the names like SPK or Speaker written near them. You just have to match the front panel connectors with that of the pins. USB pins will be near these pins and will be labled as USB5 or USB4 on the motherboard. USB front panel connector can be inserted in only one direction.
Diagonally opposite to where you connect you keyboard and mouse, there are pins to connect the front panel USB. You can identify it on the motherboard by the names USB5 or USB4 written on the motherboard. Just connect the front panel USB connector to either of these pins.