We consider the initial-boundary value problem for the 3D regularized compressible isothermal Navier-Stokes-Cahn-Hilliard equations describing flows of a two-component two-phase mixture taking into account capillary effects. We construct a new numerical semi-discrete finite-difference method using staggered meshes for the main unknown functions. The method allows one to improve qualitatively the computational flow dynamics by eliminating the so-called parasitic currents and keeping the component concentration inside the physically reasonable range (0, 1). This is achieved, first, by discretizing the non-divergent potential form of terms responsible for the capillary effects and establishing the dissipativity of the discrete full energy. Second, a logarithmic (or the Flory-Huggins potential) form for the non-convex bulk free energy is used. The regularization of equations is accomplished to increase essentially the time step of the explicit discretization in time. We include 3D numerical results for two typical problems that confirm the theoretical predictions.