We explore numerically the complex dynamics of multilayer networks (consisting of three and one hundred layers) of cubic maps in the presence of noise-modulated interlayer coupling (multiplexing noise). The coupling strength is defined by independent discrete-time sources of color Gaussian noise. Uncoupled layers can demonstrate different complex structures, such as double-well chimeras, coherent and spatially incoherent regimes. Regions of partial synchronization of these structures are identified in the presence of multiplexing noise. We elucidate how synchronization of a three-layer network depends on the initially observed structures in the layers and construct synchronization regions in the plane of multiplexing noise parameters “noise spectrum width – noise intensity”. It is shown that in a hundred-layer network, clusters of synchronized layers can be formed at certain optimal values of multiplexing noise parameters. The performed numerical studies confidently indicate that the spatial dynamics of multilayer networks can be controlled by varying multiplexing noise parameters.