Well, for one Omphalos is just a plain English word; it's not a made-up fantasy word, so that helps. But, more specifically, it's the center-point of Creation's geomancy. In Return of the Scarlet Empress, the Ebon Dragon breaks the Omphalos so he can corrupt the whole world and remake it in his image. This has the side effect of shutting down any natural defenses Creation has against the Fair Folk.
Which, as was humorously stated earlier, the book states that, ironically, this will probably be a good thing for Creation, as the Fair Folk are more likely to fight against the Ebon Dragon than anything else.
It bears mentioning that breaking the Omphalos involves killing Pasiap, the Dragon of Earth, and exploding the Imperial Mountain in the process. So, fixing it is rather difficult.