Preparing the Motherboad Tray
Have a look at the motherboard tray, the area where you will attach the motherboard. This is the side across from the one you opened earlier in a tower, and usually the bottom in an SFF. If you are working on a tower, place it on its side so you can work on the motherboard tray from a top-down view. Note that motherboard trays are removable in some cases, and following your case’s instructions to remove the tray before installing the motherboard and reinserting the whole thing can be easier than trying to install the motherboard directly in the case, if you have the option.
On the motherboard tray there will be screws with threaded sockets as heads (standoffs) that accept other screws, as well as holes where you can place more of these standoffs. Your motherboard will rest atop the screws with holes (called standoffs since they allow the motherboard to not touch the metal tray underneath it, which would cause a short circuit). Round-headed screws, not case screws, go through holes in the motherboard and into the standoffs. If there is any doubt about which screws to use, make sure they fit into the standoffs by testing one; you should be able to get the screw started in the standoff easily and without a screw driver.
Note that like screws, all holes are not created equal. The holes used to attach the motherboard to the standoffs, such as the ones in yellow squares on our picture of the ASUS P5E-VM DO, are insulated from the motherboard circuitry. We need to make sure there is a standoff under each of these insulated holes. Some of these will already be installed, screw in the remaining ones. We also need to make sure there are no standoffs in other places, they could touch the mobo in the wrong spot and cause a short. Unscrew those.
Your manuals are useful here, as they are all along. The one for the mobo will include diagrams as to exactly which holes need standoffs. The one for the case will let you know if there are any extra steps to take before the motherboard goes in. For instance, some cases have bulges under the motherboard and they include plastic or rubber stickers you apply to keep the metal bulges from touching the board, again to prevent a short. In our case, we just need to add one standoff in the hole marked by the yellow square in the picture of the motherboard tray at the beginning of this section.