It's not mission based really, that's just the tutorial. Not everything in the first area is beaten easily. The fly is basically the first boss, and you can easily go around it. The Rotworms are very tough early on as well in numbers. I suggest doing a few runs through the first area awhile before trying to tackle the boss. And make sure to save often. Especially since the game still has some crash issues.
As for the classes, how it works is you can use the secondary classes skills, but you have the attribute bonuses and gain xp to your primary class only. Passives can be used by any character in any class once unlocked.