Merge Visible Layers will combine all currently visible layers into one layer. Invisible layers aren't effected and will stay as they were before the merge. There are three ways to merge visible layers:
The final layer has the size of the largest layer of all of the visible layers. (Remember that a layer in GIMP can be larger than the image)
Will set the final layer size equal to the image size. (Remember that layers in GIMP can be larger than the image it self. If you have such a visible layer it will be clipped to the image size).
Will set the final layer size equal to the bottom layer. If the bottom layer is smaller than some of your visible layers, then the final layer will be clipped and trimmed according to both the size and position of the bottom layer.