The dynamics of matter waves in the atomic to molecular condensate transition with a time-modulated atomic scattering length is investigated. Both the cases of rapid and slow modulations are studied. In the case of rapid modulations, the average over oscillations for the system is derived. The corresponding conditions for dynamical suppression of the association of atoms into the molecular field, or of second-harmonic generation in nonlinear optical systems, are obtained. For the case of slow modulations, we find resonant enhancement in the molecular field. We then illustrate chaos in the atomic-molecular BEC system. We suggest a sequential application of the two types of modulations, slow and rapid, when producing molecules.