Animated Gif with large base image & small animated part.

Hello guys
I'm not really sure how to explain that, due to my limited English comprehansion. I will try with images.
I can easily create animated gif out of multiple layers, given each layer is identical, with small changes accuring over time.
But I yet to figure out an animated gif, that uses one large image for the base, and only small part of it is animated.
I always get the animated part working, without the large base applying across all the frames. All it does, is flashes once
the frame is reached and then moves on to being transparent, showing only the small animated part.
For example, this is a GIF made with Galaxy S4, of my friend playing with his phone, imported into PS CS6. On the Galaxy,
after I record the GIF, I can use my finder to touch, mask and freez parts I don't want to move, and leave only small, animated bit.
When I import it to PS, it shows one layer with full image, and bunch of frames with the animation part only.
http://i.imgur.com/UAiopQA.jpg
http://i.imgur.com/7XOGGV6.jpg
Problem is, once the image is open with PS, I'm not able to export it to keep it working in the same manner. Given the Samsung's
gifs are 8 to 10mb, it's hard to edit it, to make it more size friendly.
The gif clearly works the way I describe, so there is a setting or method I don't know about.
If PS is not best tool for editing GIF, what other apps would you recommand I use for it?
Thank you for the taking the time to read
best regards
Monica

This has been an ongoing issue for me since I switched from Powerpoint to Keynote. Most of the animated gifs with transparent backgrounds that I used with Powerpoint are no longer transparent in Keynote. You may want to search for those earlier threads on this topic...
To summarize: I've had to open up my animated gifs in After Effects and use the Color Key effect to restore transparency, with mixed success.
Good luck!

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