The merge options, accessible in the Layers menu (see Layer options), provide a useful way of fusing the contents of layers to form one image on one layer.
Flatten Image merges all visible layers into a single background layer, leaving out and discarding non-visible layers (the ones with the Eye switched off). At the end of this operation there is only one layer left.
Merge Visible merges all visible layers into the bottom-most visible layer, creating a single background layer and leaving non-visible layers untouched and above the background layer.
Merge Down merges the active layer with the layer below it.
The merge operations are permanent, although if you make a mistake with a merge just select Undo from the Edit menu to restore the previous state.