You're confusing the concept of Multiverses and the Omniverse.
A Universe is one universe where things happen. The Ultimate Universe, the Ultimate N-Zone, the Zombieverse, the Supremeverse, the 616-verse, etc.
Then we have a Multiverse. A Multiverse is a collection of universes that all share a space (And usually have something in common). The UU, the Ultimate N-Zone, the Zombieverse, and now the Supremeverse all share a Multiverse (We'll call it the Ultimate Multiverse). The DC Multiverse also exists, as well as the standard Marvel Multiverse.
The Omniverse is everything. Every Multiverse makes up the Omniverse. Two Multiverse can crossover (DC and Marvel, for example), but in the end it has little baring on anything because traveling to a different Multiverse is VERY difficult, and they are usually only used for Versus stories (Such as the Avengers vs the Justice League). Almost always, when two Multiverse crossover, it's out of continuity.
That clear up everything?