The multichannel generalization of the theory of spectral, scattering and decay control is presented. New universal algorithms of construction of complex quantum systems with given properties are suggested. Particularly, transformations of interaction matrices leading to the concentration of waves in a chosen partial channel and spatial localization are shown. The limiting instructive cases illustrating different phenomena which ooccur with the combination of 'incompatible' properties are considered. For example, the scattering solutions with different resonance widths at the same energy for the same interaction are revealed. Analogously, a 'paradoxical' coexistence of both strong reflection and absolute transparency is explained. The case of the violation of 'natural' asymptotic behavior of partial wave function is demonstrated : it has a greater damping decrement for the channel with a lower threshold. Peculiarities of the multichannel periodic structures, bound states embedded into continuum, resonance tunneling and degeneracy of states are described.