The Faraday instability in a system of two conjugated immiscible liquid layers with disparate thicknesses is investigated. The top layer is relatively thick and undergoes short-wavelength instabilities, while the bottom layer is thin and undergoes long-wavelength instabilities. The two layers are coupled by the kinematic and dynamic relations at the interface. Through linear stability analysis, a lubrication effect, which significantly reduces the destabilization threshold, is identified. Especially when the vibration frequency is low, the lubrication effect is seen to influence the transition between the harmonic and subharmonic instability modes. It is studied how far the system with two layers can be approximated by a single-layer system with a Navier-slip boundary condition at the bottom. In corresponding experiments it is found that the time-periodic excitation of the system creates a steady-state deformation of the bottom layer. This indicates nonlinear dynamics of the system and the violation of reversibility. The excellent agreement between experimental and theoretical results for the onset of the instability underpins the validity of the linear stability analysis.