Please see http://www.lineforeline.com/
I went crazy looking for good old ImageReady (which was where you created and edited animated GIFs) in Photoshop CS3 -- couldn't find any reference at Adobe. The basics are there under Window>Animation. You manipulate your layers/modes etc. so certain things show in certain frames.
Then, File>Save for Web...
You cannot use Photoshop to edit the animated GIF so be sure to also save PSD with layers intact. I would imagine that Fireworks would be used for editing animated GIFs but have not tried it yet.
Not sure what you mean by "stacked"?
Otherwise, what I do is have static JPEG version in place (for rollover) and have animated GIF onclick. See http://www.auntnini.com/new/index.htm