Actually, I don't think many mobo manuals come with instructions. Mine didn't, and neither did my friend's. Okay, there are several ways to do it.
First of all, you have to replace the I/O Port on the back of your case with the one that your motherboard supplied you with.
Then, you put the spacers in, which are gold in color; they should be found in the case, I believe. There are severals circular holes in your motherboard; there are similar holes in your case, but there are a lot more in your case. Imagine if you were going to align the motherboard with the holes in the case, and place a spacer in each of those holes. Make sure when you align the motherboard with the case, the holes in the motherboard have a small metal plate encircling the hole. After you place the spacers in, you should place the motherboard right on the spacers, aligning the holes in the motherboard according to the spacers. Then, place a screw in each of the holes, and fasten. That's all.
Make sure, though, that the I/O ports hook up correctly with the I/O shield.
When I did it, it was really a pain. I finally figured out what to do from like 10 online guides, and I had it all done, except I forgot the I/O shield. So, I had to take the motherboard out and place it in again, which was not fun. So make sure you don't make the same mistake as me.