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At the raised bumps the motherboard screws to them. the clips fit into the square holes where the mother board holes line up but there are no raised bumps. Also since you are new to this, only the holes on the motherboard that have metal around them are mounting holes.
The LEDs, speaker, and front USB cables will connect according to a connection map you will find in the motherboard manual. When hooking up the LEDs and the speaker the Black or White wires are the negative ones (-) and the colored wires (Red, Blue, Orange or other color) are the positives (+). However if they don't light up you can just reverse them when you turn-off the system.
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