I have a gigabyte x58-USB3 Motherboard, no screws come with it, but i have a nzxt phantom, which has tons of screws, which do i use?
Heres the screws the case has: http://www.pureoverclock.com/images/review/cases/nzxt_phantom/nzxt_phantom_3.jpg
Motherboard mounting screws come with the case, not the motherboard. Looks like yours have labels.
You first need to screw in the standoff screws. These are hex shaped,about a cm high, and usually brass colored. Put one in where the holes in the motherboard match up with the places in the case. There are usually 9 of them for an ATX motherboard.
From your case parts kit, test the screws first to see that they fit the standoffs properly. They will have a small hex head and a washer like look. If you use a screw that is too wide, it may short out by touching metal close to the mounting hole.