Can you be more specific as to what your question is if you have already read some stuff? Which part is it that you don't understand?
Basically, the front sight is your elevation adjustment. You use this to actually zero. There is a little pin that needs to be pushed down, and then you can move the sight. You can do it with a bullet, or whatever. But as you own it, and not the government, keep in mind about using metal on your finish. Tools are made specifically to move this without hurting anything. You can probably find those from Midway, and other places.If you move it up, the group will go down. If you get confused about that, use your fingers, one in front of the other to figure it out. The rear sight is your windage. Move this in the direction you need to go. Again, use your fingers if you get confused.
The rear sight will also have an elevation knob that is used to keep from doing Kentucky windage if it is set up properly. That means you can use that knob to be able to sight on normally at 500 yards if you move it to that position without changing your point of aim. The rifle will move of course, but you will still be shooting center mass. If you won't be doing things like that, don't worry about it until you want to learn your rifle better.
Look at these links, I think they might help. The target one will show you which way to move the sights. Only the number of clicks might change if you aren't zeroing at 25 yards, but the direction is the same. The other link is for the FM for M16's. Check out Chapter 5.
Honestly, if nothing makes sense, look at the target on the PDF file, and just follow it's instructions, even if you don't understand it. It will work.
http://www.bobdbob.com/~deneb/doc/targets/m16a2-25m-zero.pdf
http://www.scribd.com/doc/344690/M16-Rifle-Marksmanship