What I do is I make a canvas setting, a point where I can make all the changes and I memorize where it is in the history. I make each frame from there, once I finish a frame I flatten it all and save the .gif as "whatever1.gif" , then I go back to that point in the history and make the second frame, then flatten my layers, before saving as "whatever2.gif" and so on. It makes it a lot easier with a long animation.
~EvilNeko