My case only came with 3 motherboard standoffs.

Solution
Some cases have raised dimples for standoffs. These usually fit micro ATX motherboards.
If you have a regular atx motherboard use the 3 standoffs for the bottom three holes in the motherboard tray to line up with the motherboard holes.
You did not state what case you have so I posted a generalized answer.
Some cases have raised dimples for standoffs. These usually fit micro ATX motherboards.
If you have a regular atx motherboard use the 3 standoffs for the bottom three holes in the motherboard tray to line up with the motherboard holes.
You did not state what case you have so I posted a generalized answer.
 
Solution