You will need to align the motherboard up so that it fits snuggly into the I/O shield on the rear of the case, and then you should be able to see the screw holes line up properly.
Make sure that you insulate the screw holes with fibre/plastic washers and use standoffs to support the board and allow the installation of the 'small' screws.
Good advice for you. I would guess that some of the little prongs on the I/O shield is keeping the motherboard from seating.
Put the I/O shield in the case as a first step. Make sure it is orientated to match the motherboard ports and snaps in there tightly.
Then with the motherboard tilted slightly with the lower part going into the shield, put the part that fits in the I/O shield in first. Wiggle it around a bit until the ports fit in the shield. You may have to take your hand and guide some of those things in there.
Next, gently slide the motherboard down and outward in to the I/O shield until it slips on in to the shield area.
The next step, is to very gently set the other part of the board down flat and that should make the holes line up. Whatever you do, don't use longer screws and try to force it down. It may take a few tries to get it to slide in there (depending upon case room), but it will fit. In my opinion, when you have it lined up perfectly with the I/O shield, it just kind of slides down and in as you lower the board in front.
The screws should fit in there real well and fasten the motherboard to the case via the motherboard posts. Post back if you questions/concerns.
Important Addendum: From time to time someone forgets that they have to have motherboard posts in first. You do have those in the case to set the motherboard on, don't you?????? If not, put them in first and make sure you have one post for each hole in the motherboard (nine or so as a rule).
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