full sized ATX motherboard? There will be 9 holes, just hold the board in approximately the right location and you should be able to pick out which ones they are, or if you are good enough you can take a look at the manual and its fairly easy to match up to the holes in the case. Lining up the stand offs isnt that hard as you have limited options to pick from, just take your time and you will be fine.
I would suggest waiting until a few other components arrive to install the board though, its easier if you put the CPU, heatsink, and memory on prior to putting it in the case, that way the board isnt flexing when you push on it to mount the heatsink and install the ram.
then put the standoffs(the little brass things) in the 6 holes that match up. Screw those in until they wont go in anymore(its fairly obvious). When you put the board in screw it down until they are firm, if its taking a fair amount of force you are over tightening them. The screws actually serve to electrically connect the motherboard and the case which are both grounded to the PSU, the metal around the screw holes is necessary for it to do this so that is normal.
Yes, it is applied to the bottom of the heatsink in the form of a gray pad, make sure you remember to pull the plastic cover off the base of the heatsink before mounting it, and definitely mount it outside the case, mine required quite a bit of force and flexed the board quite a bit because i had put it in the case before installing the CPU and heatsink. Having the board on a table removes all of that risk.