PokeBuilder does not support X and Y, because the 3DS currently remains un-hackable.
However you can make a Pokemon with PokeBuilder and trade it to Gen V, then trade the Pokemon from Gen V to Gen VI with PokeBank. However, in the case that the Pokemon created is illegitimate in any way, it will not be able to get into PokeBank. Sorry. :(
Hope I helped. :)