This should go only one way. Now with plate matched up with holes in case take a black felt marker or better and mark the holes. Now you will be ready for the brass stadoffs. One end screws in the motherboard pan and the other end will sit on bottom of motherboard. Install standoffs into the spots where you marked with a marker earlier.
Screw standoffs in and set motherboard on top making sure they all match.
If all is good then take motherboard out of case. We need to add some components to it before setting it in. Installing Device Software - load your drivers for your expansion cards.