When you're mounting a motherboard in a case, usually the holes on the case won't all match up with the holes on the motherboard. Most of them will, but there will be some screwholes on the motherboard that have no corresponding hole on the case, and some holes on the case that have no corresponding hole on the motherboard. This is normal. Just use the ones that do line up, and everything should be fine. To prevent the bottom of the motherboard from touching the metal case, you have to screw little tiny brass things called standoffs into the case, then screw the motherboard into those.
Tip for the day: it is very important that if there's a hole on the case with no corresponding screwhole on the motherboard, you don't put a standoff there! I was installing a motherboard into a used case that already had some standoffs, and I neglected to remove one. Bad. Luckily, no permanent damage was done - after I unscrewed everything, found the extra standoff, removed it, and put everything back together, it worked again. Scary experience though! Not only would the system not POST, but there was a strange quiet buzzing noise coming out of the speaker.
Anyway, everything works now, and I'm going to bed.