Install the modules, then run the update. At least that's what I did.
When you go through the installation wizard for BS2, make sure you select "Black Shark 2 Upgrade version" when it asks what serial version you want.
And no. This is not IL-2 1946, you don't have to install all the updates one after the other :P Simply download the latest 1.2.8 version of everything and install into the latest version of DCS World.
The method that uboats posted looks really simple, I didn't even know you could do that I'll try it next time I buy a new module :)