First answer to saving it in a type that supports layers.  You did already its a .png (a png will save all layers), the other one is a .jpg (a .jpg does not, it merges everything into the canvas.  However, you need the finished .jpg for Poser's material room).  Load you .png image and you will see the original base and back layer.  Load you .jpg and you will only see the base and back layer merged together, since the back layer is not active, you see only the base.

Now for your second question:  Understanding layers.

I guess the best way is to show examples.  I'll work something up.  Mine will be done in PaintShop Pro since I don't have Gimp.