Photoshop workflow? Manually filling shapes...

Hi!

I'm getting a little more used to Photoshop (I use CS5) but I'm still very much a newbie. I'm in the process of trying to color the line art of an animated short. I attempted to use the Fill tool, but because all of the black-and-white line art is anti-aliased, the fill tool leaves that thin little blurred line of anti-aliasing uncolored. I've tried to push the tolerance of the fill tool, but even when I've maxed out tolerance, there's still a little line of anti-aliasing that isn't filled in.

What I've ended up doing is basically coloring the line art manually, on a layer behind the line art. Given the hundreds of unique drawings in the short, it's a huge time sink. I know I'm probably wasting a lot of time, but for the life of me, I can't figure out any other way. Does anybody know a more efficient and effective workflow for coloring in the b/w line art?

Thanks, Photoshop sages! If my explanation is unclear, I'll reply with some screencaps to demonstrate, but I think y'all probably get the idea.