In this article, we explore the dissipation dynamics of a strongly coupled multidimensional system in contact with a Markovian bath, following a system-bath approach. We use in this endeavor the recently developed stochastic multi-configuration time-dependent Hartree approach within the Monte Carlo wave packet formalism [S. Mandal et al., J. Chem. Phys. 156, 094109 (2022)]. The method proved to yield thermalized ensembles of wave packets when intramolecular coupling is weak. To treat strongly coupled systems, new Lindblad dissipative operators are constructed as linear combinations of the system coordinates and associated momenta. These are obtained by a unitary transformation to a normal mode representation, which reduces intermode coupling up to second order. Additionally, we use combinations of generalized raising/lowering operators to enforce the Boltzmann distribution in the dissipation operators, which yield perfect thermalization in the harmonic limit. The two ansatz are tested using a model two-dimensional Hamiltonian, parameterized to disentangle the effects of intramolecular potential coupling, of strong mode mixing observed in Fermi resonances, and of anharmonicity.