You can choose in the options for layers to merge a selection of layers, or flatten layers. Flattening seems to just do what merge does but for every layer in the document (right?). But does this do anything else? And it seems that the overlaps happen in the precedent top down in the layer list.
So I just want to know if there is anything else about these two options that I don't know about. They do seem useful if you want to organise a complex artwork.