Lithium-ion batteries (LIBs) are the main energy storage devices that have found wide application in the electrical, electronics, automotive and even aerospace industries. In practical applications, silicene has been put forward as an active anode material for LIBs. This is facilitated by its high theoretical capacitance, strength, and small volume change during lithiation. Thin-film materials containing two-layer silicene and intended for use in the LIB anode have been studied by the method of classical molecular dynamics. Among the important characteristics obtained is the fillability of the silicene anode (under the influence of an electric field), which was determined depending on the type of vacancy defects in silicene and the type of substrate used. Both metallic (Ag, Ni, Cu, Al) and non-metallic (graphite, silicon carbide) substrates are considered. The behavior of the self-diffusion coefficient of intercalated lithium atoms in a silicene channel as it is filled has been studied. Based on the construction of Voronoi polyhedra, the packing of lithium atoms and the state of the walls in the channel has been studied in detail. The change in the shape of silicene sheets, as well as the stresses in them caused by lithium intercalation, are analyzed. It has been established that two-layer silicene with monovacancies on a nickel substrate is the most optimum variant of the anode material. The results of this work may be useful in the development of new anode materials for new generation LIBs.