Considering the entire human race (all 6.5 billion or so) could fit on the island of Zanzibar if standing up, and thus could, if so arranged, be conceivably completely exterminated by a single nuclear weapon (in the 10 - 25MT range), to my mind, the simplest way of committing genocide and covering it up would be to simply haul all the people you want to get rid of out to the middle of nowhere, and happen to test a device at the same location.
Nuclear tests are inherently secret and two great tastes surely taste great together. Quick, cheap (assuming you have the bombs) and no evidence left over except the paper trail, which is easy to get rid of. Anything less is really just inefficient, honestly. Failing this, really large amounts of conventional explosives work well too. Particularly if arranged to produce, say, a giant sinkhole underneath the target. Setting up camps and what not is barbaric and crude - if you're going to do that you may as well use them as forced labor.
Actual genuine conquest of disagreeable territories can be a wholly seperate matter altogether (such as, say, taking all the intellectuals and shipping them off somewhere like, oh, the Taklamakan) depending on how one wants to go about it. But generally, when committing genocide, it's best to have a way to do it quickly and instantly, I think. Otherwise it just breeds resentment and gives your enemy a reason to resist you further. I've historically never bothered with it at all, as a result, personally.