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Disclaimer to Jam this post has nothing to do with my small form factor computer but instead out of confusion that i would like cured.
ok this is probably stupid question but when you buy a new motherboard how do you install it in the case so the PCI slots meet up with the opening? i know that for the ports and all your given the metal rectangle thing that you replace but what about the pci slots?? i was thinking about it and all i can come up with is PCI extesion cord :P but that probably does not exist so how do you get the pci slots to meet up??

The assumption by the motherboard manufacturer is - you are using a modular (ATX) case (with provision for at least two PCI slots) or more, so they don't have to worry about that because their schematic design already incorporates that.
If you have something that isn't universal then the problem & a workaround is solely your responsibility.

The standard ATX case has numerous holes in the motherboard mounting plate to accomodate different size motherboard. Before you can mount your motherboard you have to find which holes in the plate line up with the ones in your motherboard. You then insert the hex-shaped standoff screws in these holes. You place the motherboard on top of these standoffs. Finally you insert screws through holes in the motherboard through to the standoffs to hold the motherboard down.
Note that mid and full size cases can accomodate almost any standard size motherboard. Smaller cases are limited to how large the motherboard can be. You have to check the case specs to see what these limits are.

Are you sure you want to want to put in motherboard by yourself? I'm sorry but the questions you are asking are very logical.
AMD Athlon 64 X2 4400+ OC 2.7ghz
2GB Dual Channel DDR 3200
Nvidia 7800GT
SATA II 2x 200gig 7200rpm 16mb cache RAID-0
Gigabyte Nforce 4 SLI

it's not that i want to place one in i was just curious how are people suppose to do it but i guess the universal ATX case thing works my questions is answered

If you really are going to attempt this. Put a little black tape on the back of your mobo over the mounting holes with a small hole for the screw to pass through (or any vulnerable spot). So when you have difficulty aligning something up you won't be scratching the delicate foil runners off the back side of your brand new board. Rarely there are a couple of tangs by the upper USB and mouse/keyboard ports. if they aren't in first you will have a hard time later after you already put screws in.
correct me if I'm wrong

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