If the layers are overlapping, have you messed with blending modes? Sometimes a certain blending mode will do just what you want.
You could select a layer, double the rectangular mask tool, making a mask the size of the layer, then “M” and twirl down to Mask Feather and it seems better if you put a small negative number on Mask Expansion too, then the edges of that layer would be soft. If you only want the vertical edges soft, double click the mask then pull the transform box (like PhotoShop Transform) until the top and bottom of the mask go above and below the layer. Then only the ends will be soft. You could also try roughen edges on each layer.