Likely, you are having trouble seating the motherboard because of the rear I/O panel.
a. First verify that each of the case standoffs are properly inserted.
There should have been no reason to remove them.
b. Check that the case standoffs match the motherboard.
If there are any case standoffs that do not match, remove them.
c. Hand thread your screws into the motherboard standoffs to verify that you have the right size.
A case will come with several screws that look alike. If you are missing what you need, go to a store and buy some or contact the case maker for replacements.
d. The tricky part with installing a motherboard is getting the rear panel to accept the motherboard.
The rear panel may have some spring tabs that need to be compressed. A second pair of hands for this process can be helpful.
Push the motherboard into the rear panel and hold it there while you insert the first screw.
One near the i/o panel is best to do first.
The next one should be on the opposite side . You may need to rotate the motherboard using the first screw as an axis to get all of the holes to lign up.
Do not tighten any screws until you get them all threaded.
I find that a #2 magnetic tip philips head screwdriver is most helpful for assembly.