Your supposed to use the ones on the left for motherboard. Make sure the standoffs are screwed into the case very tightly, then you just snug the screws in. If you put the screws in too tight the standoff will just spin when you try to removed them.
Did your case not come with directions for which screws to use??http://www.pureoverclock.com/images/review/cases/nzxt_phantom/nzxt_phantom_3.jpg