The standoffs are screwed or inserted into the chassis, and the mobo in turn is attached to the standoffs through the mounting holes in the motherboard. This creates a small space that prevents the back of the motherboard from shorting out against the metal case.
Don't be surprised if your motherboard has "extra" holes for which there are no corresponding holes in the case. This is normal. Very few cases and motherboards will match exactly. As long as you use all the mounting holes that do match, you'll be fine. (And there's no charge for the extra holes.)
Standoffs should NOT be inserted into any "extra" holes, however. Standoffs installed in holes on the case that have no corresponding holes in the motherboard can cause the motherboard to short out. And don't over-tighten them. Hand-tight plus a smidgen is enough.
