This guide was written using my 2007 R6, the 2006 should be identical. 2008+ will be similar.
Torque Specs:
Smog Plate Bolts - 7.2 ft-lbs - Loctite Recommended (Blue / Medium) (Taken from the 2007 R6 FSM)
There are two methods of installing smog block off plates, the air box method, and the radiator method. Note that no matter which way you choose removing the fuel tank is still pretty much mandatory to plug off the air box side. Also as a heads up, the fuel tank does have a check valve, so you can disconnect the line and only a little gas will leak out, draining the tank is not necessary.
Air Box Method
Once you remove the fuel tank, you will be able to completely remove the air box. This will then allow you to remove a small plastic panel in the frame that will allow you to access the spark plugs, and smog plates.
This method can be very time consuming as the factory bolts do have loctite on them and won't come out easy. It is critical that you get your allen wrench in the bolts square, and completely to prevent stripping the heads.
Radiator Method
Removing the radiator does require you to take the lower half of the bike apart too. This method is more work, but I feel that it makes the job easier, and therefore worth the extra work. Also it gives you a chance to change your antifreeze (supposed to be changed every 2 years, or 16k miles which ever comes first), and allows easy access to the spark plugs if it's time for replacement (spark plugs are replaced every 8k miles).
Finalizing the Install:
There is no "gasket" for the smog plates, there is a rubber seal around the reed valves that seals against the smog block off plates. Also note that several of the block off plates sold are directional. Graves plates for example have a machined out area to clear the screws in the reed valves, if you install them backwards, they won't seal, and you'll have a bunch of extra noise from them. On the Graves plates if you are sitting in front of the bike facing the motor the "G"s should be readable (not upside down). The solenoid (the one the hoses run to) that is attached to the plastic panel in the frame came be completely removed, just unplug it and remove the push pin holding it in. Also the plates should have come with a rubber cap to cap off the port in the air box that used to go to this system.