Since you already have an atlas, I'm guessing you don't want tk2d to re-atlas it?
If so - check out the runtime sprite collection sample, which creates a sprite collection at runtime from rectangles within a texture.
After you've got a collection, you can create a tk2dSpriteAnimationClip and play that directly.
If you want to do this in code, but then set up animations, etc. in the interface, its still doable. Let me know if thats what you want.