The motherboard can go in only one way. Do not force anything.
1. mount the motherboard rear panel plate in the opening of he case. It is a press fit, and you need to push firmly all the way around to seat it properly.
2. Position the motherboard so that the rear ports match up with the I/o plate. Note where the motherboard holes match up with where the standoffs are. That is where to insert standoffs. Do not put in any standoffs where there is not a matching motherboard hole, or you will cause a short.
3. To install the motherboard, you need three hands
One to hold the motherboard in place, one to hold the screw, and one to hold the screwdriver. I solve this with a #2 magnetic tip screwdriver. Do not tighten the screws initially. Get them all in, then tighten them one by one.
Snug is enough. If you overtighten, you may later have a hard time removing them without undoing the standoffs too.