We analyze the impact of multichannel scattering in harmonic waveguides on the positions and widths of confinement-induced resonances for both isotropic and anisotropic transversal confinement. Multichannel scattering amplitudes and transmission coefficients are calculated and used to characterize the resonant behavior of atomic collisions with varying anisotropy. A mechanism is established which leads to a splitting of the confinement-induced resonance in the presence of anisotropy.