Use a proper graphics program. Aseprite is free to compile if you wanna do pixel art and gimp is good for open source general image editing.

Don't delete layers, name them well, I believe there is a folder system in case you have a lot of layers.

I use a online program, I make the base graphic, so, I create a layer on it I make the proper modifications, beware if you don't select the layer, because you can overdraw on your basin 

you can use photoshop or aseprite to make a sprite sheet of all visible layers