The base shear is "at the base" and should include the entire weight of the structure. But if you are designing various parts of the structure, you will not simply take the total base shear and use it throughout the structure.
Some examples -
If you are designing the roof diaphragm, you'd want to include the roof dead load and the upper half of the two walls which are perpendicular to the direction of loading as this is the load path that goes THRU the diaphragm.
If you are designing and exterior wall for seismic forces perpendicular to the wall you'd only include the wall self weight.
If you are designing the two shearwalls which are parallel to the seismic force, you'd include the upper half of the perpendicular walls (the lower half mass force goes straight down to the ground) and include the roof dead load as well as the shearwall self weight. The connection between the shearwall and the roof diaphragm would NOT include the shearwall self weight.
If you are designing the lateral resistance to building sliding you'd include everything.
Just be sure to correctly visualize the load path that each little "piece" of the building mass takes to get "down" to the ground and this helps to ensure the proper value to use.