Load Both Layers, Load Only A>, and Load Only B When you load a sysex file, receive a dump or merge from your Prophet 12, or reset your patch, your setting here will dictate whether this will effect both layers, or just Layer A or Layer B (keeping the other one intact). This way, for example, you can just clear out Layer A. Or you could make a patch consisting of the Layer A of two different patches, by first loading one patch, then copying its Layer A to Layer B, then restricting loading to just Layer A, and then finally loading the second patch.
Note that BPM, Split Point, and A/B Mode are only associated with Layer A, and Patch Name is only loaded if you're loading both layers.