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I found the System Panel Header, now I just need to plug em' in.

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If they aren't labeled check your manufacture sheets they should be labeled there if not trial and error – 50-3 Oct 15 '13 at 22:22
For your question: yes, it does matter. Not only it matters where you plug them in, for some connectors it also matters in which polarization they are connected. – noggerl Oct 15 '13 at 22:40
up vote 2 down vote accepted

What you're looking for is the "System Panel Header" on that picture you gave, #16. If you grab the "Quick Install Guide" from, you'll find the pinouts for the header on Page 23 (edit: bottom of page 23) (second edit: the picture in question is on page 2 of the quick install guide, since the link was removed.)

The two important ones are "PWRBTN" and "RESET". Connect the appropriate button's jumper to the labelled header, and the other side to one of the "GND" pins.

PLED/HDLED are for the power and hard drive lights - the jumpers in that bundle of cables should be properly labelled with + and -... just match 'em up.

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