To clone a Pokémon in X and Y, you need two 3DS consoles, and two copies of the game, as to clone the Pokémon, you need to trade them.
Say you have an Arceus that you want to clone. I will call the game with the Arceus game 1, and the other one game 2. To clone Arceus, trade it from game 1 to game 2 with a Pokémon that is expendable, such as Pidgey. Start the trade, and in the middle of it, while the screen is black(I think), soft reset. The timing here is important, and it may take several tries to get it right.Be warned that the Pokémon from game 2 will disappear, and that is why I said it has to be expendable. This method can also be used to clone items.
There are many YouTube videos on how to do this, so I suggest you watch them to get the timing correct. The best tutorial on this glitch, in my opinion, is this. I highly recommended watching it if you are going to perform this glitch.
Source: I watched the above video a while ago, and also this.
Hope I helped.