The construction of physical occupation and transition probabilities in non-Hermitian, effective-Hamiltonian models of coupled near-resonant discrete states which decay to a continuum is analyzed. We consider for definiteness the particular physical example of atomic multiphoton ionization. The possibility of finite duration and arbitrary modulation of this interaction, and of the subsequent ionization and/or decay, in such a system allows us to invoke switching considerations in conventional $S$-matrix theory. The effective Hamiltonian $\stackrel{^}{H}(t)$ is derived for both stationary and time-dependent Schr\odinger equations. These derivations yield the same effective $\stackrel{^}{H}(t)$, and further reveal that this operator is associated with discrete-state-projected scattering states. The Hermitian conjugate operator ${\stackrel{^}{H}}^{\ifmmode\dagger\else\textdagger\fi{}}(t)$ is similarly shown to be associated with discrete-state scattering states. This shows that effective-Hamiltonian theories are intrinsically $S$-matrix theories. This fact, in turn, is employed to construct transition amplitudes. The possibility of resonance in the atom-field interaction requires that both the projected incoming states and projected outgoing states be employed in this construction. The projected incoming and outgoing states in the (discrete) bound space are quite conveniently described by effective time-dependent Schr\odinger equations, supplemented by initial- and final-state boundary conditions. The fact of independent-exponential decay from each mode throughout the history of the interaction, for an arbitrary initial superposition state, in the adiabatic limit, suggests a practical construction for intermediate-time bound-state probabilities. This construction permits the formal definition of individual-state probabilities, which satisfy a generalized adiabatic theorem, and leads to the satisfying result that the total bound-state probability at all intermediate times is the sum of complex-mode probabilities. In marked contrast to the conventional norm-of-state definition of nonionization probability, this sum does not have oscillations at intermediate times, in the limit of adiabatic modulation of the interaction. Superposition-state probabilities, however, exhibit oscillations at intermediate times. The resulting non-Hermitian quantum dynamics is especially suited, and even essential, for an accurate description of near-resonance ionization. Precise matching of the time-dependent $\stackrel{^}{H}(t)$ and ${\stackrel{^}{H}}^{\ifmmode\dagger\else\textdagger\fi{}}(t)$ with bases of their instantaneous eigenstates is required by approximate unitarity in the discrete decaying space, for a consistent theory. We illustrate these considerations in a general way in the context of resolvent-operator techniques. The implementation of the theory in both its time-dependent and stationary-state formulations is presented in an Appendix, for the completely general two-state non-Hermitian Hamiltonian. The results of these formulations are found to agree, in the adiabatic limit, to all orders in the non-Hermitian interaction. The utility of direct diagonalization of the effective $\stackrel{^}{H}(t)$, advocated by Armstrong and Baker, is transparent. The overall context of interpretation of their earlier work is, however, significantly altered. Similar considerations apply for nonswitchable interactions, such as for $K$-meson decays. These results represent a practical generalization of quantum mechanics to non-Hermitian systems. The utility, and the necessity, of such a generalization has considerable theoretical interest, and direct experimental implications.