Universes are like sections of a website. Every universe has a backstory, characters (cards) and scenarios (boards).
In the original version of the Kobol engine, universes where tied to realms. In the remake, we detached them to ease sharing and allowing artists to make mashups with elements from other universes.
To have a better understanding of how universes work, take a look at the original PoliCromix realm options:
PoliCromix univese selector featuring the X Universe and Yggdrasil
The "X Universe"
The story of the X universe was about the "Cariñopatos", creations of "El pato", a god that arrived to a world and forced everyone to love him. When people got fed up of the god, they created the "evil soaps" that started to wash out the god's minions.
This universe had a single board with two variations and a handful of characters that inhabited the world.
Yggdrasil
This universe was based on the norse mythology, had several boards based on the different worlds and a handful of characters but no backstory.
Some character cards:
Though both universes were separate things, both were shared among all realms, so players could create PvP matches in one universe using that universe boards but allowing cards from the other universe to be played:
A PvP match in an Yggdrasil board with cards from both Yggdrasil and X universe