I've played the dragon campaign with my friends and we think it's pretty awesome. I also have the one about the rune priests but I don't know how to replace the main one with that one. Can anyone help me?

You mean Cult of the Rune? Didn't your said expansion come with a rulesheet? The new Challenge cards from the expansion don't replace the base game Challenges, you still use those, apart from the Red Challenges (which might be used).

If you don't have the rules, one of the "wave of expansion packs" links should have the Cult of the Rune rules:

www.fantasyflightgames.com/edge_minisite_sec.asp

Dam said:

Exactly, your expansion should come with the rules, tokens and cards. The rules clearly state what to replace from the core set.