I ran a wfrp campaign where one of my players was Sigmar Reborn (Valten, but he was called Hanz). They gathered troops, solved tensions with the churches, made alliences with the Elector Counts etc. On the other hand they played some Skavens. They had to prepare utter annihilation of the humans, come up with a cunning plan for world domination and try to stay alive while being tossed between clans, fractions and enemies.
I ran my campaign this way because one of my players was only OG available between 15 and 21 hours, wheras the other players were available drom 11 to 21. The skavencampaign ran from 11 to 15.
This campaign ran for two years, so I now consider myself an expert in split campaigns
Some events that might inspire you:
One time the skavens prepared an assassination on an ally of the humans. They had to kill a priest, Luther Huss, who was being garded by some freelance humans (the players). The skavens prepared a plan, assigned their troops and took possition. Then my other (late) player arrived. So we switched to the human campaign. He led the humans in defending their package (Luther Huss). The other players followed his leadership and commands. The human player had no idea his friends had only hours before devised the attackplan of the skavens. I must say that all my players played excellent. Most funny moment was when the Slayer killed the Rat Oger that was actually the mutantpet of his own Moulderskaven. He was happy and sad at the same time.
I had twisted the plot in the end that some chaos-betrayal made the skavens sitting on the same side as the humans, without the humans knowing this. The players didn't know this either, because i like to play with timelines: the humans were suddanly getting help from their own skavens (that i controled), and only later did they play the scenario with their skavens that explained why the skavens needed to protect the humans. In the battle i allowed players that went down (unconsious, entangled, dead) to continue playing with their skavens.
When one group didn't understand why things were happening, i used to other group to explain things. For instance: the humans were being followed. They didn't know by who or why. I'm sure i had some brilliant idea at the time, but being a GM that prepares very little and invents an the flow, i sometimes forget things. So i forgot between sessions that they were being followed. But my players remembered weeks later and searched for reasons. The whole story was about to derail when i had their skavens encounter a Eshin-party that had trailed the humans, just for information purposes. The human characters still didn't understand things IG, but at least they stopped to try to explain the events so vigourasly (because the players already had the answer). You might call it bad roleplaying, but none of us had any problems with it and i was happy that my campaign was back on track.
Mostly I used both groups to tell the greater story without the need to resort to deus ex machinas. I told the story of the dwarfs, the humans and the elfs in the human campaign, wheras i explained the choas-side with my skavens. In the end the players experienced an epic adventure. The empire was saved, the human characters are all dead, and all of my players keep asking for some more skaven adventures.
But first they'll have to serve the emperor for some time...
ps: I tried to keep my English as tidy as possible. Be gentle, or this first post will be my last and i'll return to leeching these fora