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Cavity optomechanics and electromechanics form an established field of research investigating the interactions between electromagnetic fields and the motion of quantum mechanical resonators. In many applications, linearised form of the interaction is used, which allows for the system dynamics to be fully described using a Lyapunov equation for the covariance matrix of the Wigner function. This approach, however, is problematic in situations where the Hamiltonian becomes time dependent as is the case for systems driven at multiple frequencies simultaneously. This scenario is highly relevant as it leads to dissipative preparation of mechanical states or backaction-evading measurements of mechanical motion. The time-dependent dynamics can be solved with Floquet techniques whose application is, nevertheless, not straightforward. Here, we describe a general method for combining the Lyapunov approach with Floquet techniques that enables us to transform the initial time-dependent problem into a time-independent one, albeit in a larger Hilbert space. We show how the lengthy process of applying the Floquet formalism to the original equations of motion and deriving a Lyapunov equation from their time-independent form can be simplified with the use of properly defined Fourier components of the drift matrix of the original time-dependent system. We then use our formalism to comprehensively analyse dissipative generation of mechanical squeezing beyond the rotating wave approximation. Our method is applicable to various problems with multitone driving schemes in cavity optomechanics, electromechanics, and related disciplines.