The nuclear time-dependent density functional theory (TDDFT) is a tool of choice for describing various dynamical phenomena in atomic nuclei. In a recent study, we reported an extension of the framework - the multiconfigurational TDDFT (MC-TDDFT) model - that takes into account quantum fluctuations in the collective space by mixing several TDDFT trajectories. In this article, we focus on technical and numerical aspects of the model. We outline the properties of the time-dependent variational principle that is employed to obtain the equation of motion for the mixing function. Furthermore, we discuss evaluation of various ingredients of the equation of motion, including the Hamiltonian kernel, norm kernel, and kernels with explicit time derivatives. We detail the numerical methods for resolving the equation of motion and outline the major assumptions underpinning the model. A technical discussion is supplemented with numerical examples that consider collective quadrupole vibrations in $^{40}$Ca, particularly focusing on the issues of convergence, treatment of linearly dependent bases, energy conservation, and prescriptions for the density-dependent part of an interaction.