First and foremostx tbe misconception that more power phases spreads out the power and runs cooler has never been true. It doesnt work like that at all. With less phases, the mosfets are much further apart, so the influence from one to another is reduced. Cram 13 side by side, or 10 for the ftw, and the influence is increased.

The thermal pad modification is said to be optional. If you dont want to install it, you dont have to.

Removing a small piece of the thermal pad for the backplate will not hurt anything. You can easily do that and still install it.

For the vrm section being completely different, that is normal, but i have not seen the classified pcb in person. The classified typically uses completely different mosfets and chokes since it is 100% meant for exotic cooling measures. The mosfets are still in the same location and would still have a thermal pad across them. The FTW even has a thermal pad across the mosfets, but most people assume it doesn't because the internet said somewhere that it was missing, although that is wrong.

The thermal pad that EVGA supplied would go above the original thermal pad on the other side of the heat spreader and theoretically transfer heat from the heat spreader to the cooler.

The instructions tell you how to install them on the classified. If you are going to install the thermal pads, follow the instructions in the thermal pad modification thread that is stickied to the top of the forum.

I agree completely with jordanjb, I have just installed the thermal pad mod on my 1080 Classified and steps II and III are not applicable at all. It is not just a question of following the instructions. The Classifieds are very different from the FTWs, I wish I had detailed instructions of those steps for the Classifieds only as I am not sure if what I did is the best for the card. 

I am also in the same boat.
 
My new heatsink arrives today so I want to do the MOD but the online instructions seem different from the ones I received with the pads in the post.
 
I think the instructions I received in the post are correct though, and the online instructions are wrong (as they keep mentioning this big long thick piece of rubber for the VRM) but my kit doesn't have anything nearly as big as that. (that larger bit isn't included in the Classified instructions I got in the post with pads).
 
Don't see why the Classified instructions couldn't of been posted online in colour, as the FTW ones were?  The photocopying quality for diagrams isn't great on the instructions I received with the post (due to black & white only)

backplate pads (up-close)

Classified Thermal Pads Manual
Page 1

Thank you very much friend, indeed those are the correct pads with their instructions, they are completely different from those of the ftw.

Greetings.

No, thank you, very kind, that's more than enough. Greetings.

okay no worries; I'll leave it up there anyway in case anyone else is curious.  (I was the same as you at first) because all the instructions found online up until now do only seem to concentrate on FTW.  So at least there's something online now for Classified too :-)
 
Good luck.

I never got the thermal paste mate; think it must have just been missed on the assembly line. 
 
Not a big problem though (I had a couple spare) and they're easy to get and cheap to have delivered.
 
They did however give me a free bag of paste with my replacement heat sink though.
 
So I can't complain. My heat-sink issue was also dealt with very well by EVGA.  A+