This is gonna sound dumb but this is the first time I've dualed any of my characters and I'm geting kinda worried that I did something wrong. I dualed Imoen at level 5 to a thief/mage, but now she's a level five mage too and still doesn't have any of her thieving abilities. When do they stop being inactive?

Read the part about Dual-Classing again: The 1st class is reactivated when the 2nd class's level surpasses the level at which you Dualed. You do know that Imoen will never again Level Up as a Thief, right?

Nick's Axiom: Read the manual twice before trying anything.

Yep, when Imoen hits level 6, you'll get the theiving abilities back. Although I believe she can't cast spells wearing armor, so you will have to keep her in a robe.