David:
I'm using LViewPro which allows me to edit "layers" in a GIF89a file. It allows for animations (yes, I understand that paint.net doesn't support animation) by having different images on each "layer" and allows them to be displayed in sequence and looped if desired.
Maybe the LViewPro isn't using the right term for what it is calling a layer but it appears to me that the end result is the same.
Thanks
Jerry