33 minutes ago, Tubby94 said:

I get that I can create new world and MVP matrices to separately  describe the positions, but it still doesn't solve the problem of how I tell the shader to use MVPA on the cube and MVPB on the pyramid.

Because between the draw of the cube and the draw of the pyramid, you change the matrix to use, it is not a concern of the shader, it is a concern to change the constant buffer view to a different value ( and because you are doing DX12, deal with memory life time of buffer content ).