Oops! seems I missed your question a little.
For attaching your animated texture to the character, all you really need do is select one of the images in your sequence, switch over to the Animations tab, then on the Mesh tab, under the Skin area, click Use on the material you want it to be used on. The texture package itself will contain all the frames. It may look like each one is animating, but in reality they're just displaying the info they're given. You may notice each one is a frame off from the one above it. It's been that way in my experience, anyway, though my sequences weren't very long (like a fraction of a second, maybe 8 or 9 frames).
The only way to arrange them so that they aren't in your way is to arrange them into groups so that you can select, say, your animated files only, or your face textures only. Then you save the animation file (.ukx) and your texture package (.utx). Remember to define the textures in your .u file, or the textures won't show up properly in-game. Check existing .u files for samples of this.
Your resulting texture package will no doubt be larger than most other skin packages, though.
Most of the animated shaders you see utilize a lot of texture modifiers and combiners. The main ones you'll probably end up using, though, are TexPanner, TexRotator, and TexOscillator, along with Combiner and Shader. Using these to animate textures typically results in much smoother animations as well as lower texture file sizes.
If you want, I can write a small tutorial to help you get started. Otherwise, most, if not all of the info you'll likely need to get started is at the link in my last post.
-Tj-