After mounting all of the stand-offs, it's just a matter of mounting the motherboard as you normally would.

For this part, I used an old motherboard I had sitting around.  I didn't want my new mATX board damaged if I accidentally spilled acrylic glue.

I also mounted a PCI card to insure that the notches for expansion cards lined up properly.  The PCI card will also serve to help keep the rear panel lined up while I glue it.

Mounting the rear panel is simply a matter of lining everything up.  Notice that the bottom panel is larger than the overall dimensions of the case.  There is a reason for that, and I'll cover it in a later guide.

Because the motherboard and PCI card should rest flush against the rear panel, I used my two clamps to pull the panel against these parts.  The small piece of bronzed Plexiglas shows me that the panel is square with the bottom of the case.  I used a right angle square to make sure that the panel was straight up and down with the base.