All Roman Emperors were treated equally, and each respected the others' rights to rule as master of their own world. However, since Roma I was more advanced and dangerous than any of the other worlds, its emperor was always given the most influence. Germanias liberated during the war were incorporated into the Empire under the dominion of this "Prime Emperor".
Many Romas were not a part of the Empire. Fifty Romas chose to isolate themselves, either because they were extremely enlightened and wished to remain intellectually pure, or because they were superstitious or xenophobic. Another 100 were left behind because they were seen as not having anything to contribute to the Empire, usually because they were ruled by tyrants, depopulated by a natural disaster, or too backwards to justify the effort.
By the end of the war, over a billion people had died, and the Empire included two thousand versions of Earth. The resultant power of the Empire made the Great Houses afraid it would fall under enemy influence, prompting House Mirraflex to try to erase all of the Known Worlds. However, with the help of Abschrift, Marcus Americanius Scriptor was able to seal away and protect the Roman universes. He was left in charge of policing the German worlds to stop travellers between them. (PROSE: Warlords of Utopia)