sincreator :
You should use ALL standoffs. They are grounding points for different components on the motherboard. I didn't install all of them one time before and my soundblaster sound card started shooting sparks out. They told me at the shop that all standoffs need to be installed and the backplate is a ground also. That was 8 years ago now and I always recommend installing all of them now.
Also if your screws aren't lining up then you most likely have the motherboard improperly installed. Usually that is what causes them to not line up. Make sure that the backplate is lined up to the motherboard inputs properly. That is usually where it brings up causing a misalignment.
Yes, you SHOULD use all the standoffs but it's not absolutely necessary - one of my previous matx cases didn't even have all the required holes for my board, didn't stop it working just fine for 2+ years though