Some thoughts about this...
Obviously, having two people control the entire empire at the same time is doomed to failure. You'd have planets attacking themselves and fleets trying to go in two directions at once. It'd be chaos.
However, it might work (and would be very cool) if you designated one player as the "Leader," and the others as his "Admirals." The Leader controls the entire empire and can give orders to anyone, but he can also assign control of specific planets or ships to his Admirals, who would then fight battles and manage planets for the greater good of the empire. For example:
Emperor Fred, Leader of the People's Democratic Republic of Fredland, has a massive empire that spans two galaxies. He is at war with two other, similarly large empires - the Kingdom of Andromeda and the Earth Federation. Obviously, despite being a god in human form, Fred cannot be expected to manage all the Happy Free Slave Worlds of his Republic and fight two major wars all at the same time.
Fortunately, Fred is not alone. Under his command are the daring Admirals Bob and Steve, and the slightly-less-daring Admiral Mike. Admiral Bob is assigned control of the forces assigned to fight Andromeda, Admiral Steve is placed in charge of conquering Earth, and Admiral Mike is left with managing the Happy Free Slave Worlds, while Fred coordinates the offensive.