Many have pointed out that base and morrsleib can't be combined...
You can do whatever your little heart desires. If you combine them or make special decks using a little of both sets the FFG game police are not going to drag you away.
We've been using specially built Chaos Card decks and selected upgrade cards from both sets for dozens of games and having a blast.
Try it out. If you've always thought a certain card was overpowered, swap it out. Or, if you think a certain god isn't as good as the others, then try to give him the best cards of both sets. Be creative! You'll find it more fun than either of the preset chaos decks/upgrades. We never play the presets anymore.