Base - Can be used without the top if you just want something to hold the controller down.
Center hole is for a m3 5mm bolt to self tap and hold the PCB down, if you want to use the side tabs to hold the case down.
Otherwise you can take a longer bolt and mount it via the center hole only.
Top - If you want more protection, but still have the ability to adjust the temperature pot and still provide the heat sink with fresh air, add this to the base. It will need M3 20+mm bolts. You will need to rotate the part and add supports for the m3 bolts.
Standard has a 4mm hole, there are files for 5,6,7,8,9,10mm holes.