Layout all your parts in a clean area.
Use a sheet of tissue paper to lay your secondary mirror on face down.

Lay two toothpicks across the back of your secondary, or find some similar thickness substitute. Toothpicks are ideal because if you are unable to pull them out when the silicone is cured, you can just break them off! Apply a small amount of silicone rubber on the back of your secondary and gently apply the secondary holder on top of the silicone rubber; make sure that the secondary attachment screw is in the holder. The toothpicks will give the proper spacing between the mirror and the holder. This ensures that no stress is passed through from the holder to the mirror.

 

The next steps are optional and at your own risk, but I find the payoffs to be worth the effort.

Again lay the secondary mirror face down on a tissue. Use the flattest black spray paint that you can find. Holding the can at a high angle, spray once all around the secondary. This should cover the aluminized sides of the mirror and the silicon, preventing unwanted reflections and diffractions. Do not over spray, this will cause the mirror to stick to the tissue on the sides. Rather wait till it is dry and do a second coat.