Amplitude models are applied to studies of resonance structure in $D^0to K^0_S K^- pi^+$ and $D^0to K^0_S K^+ pi^-$ decays using $pp$ collision data corresponding to an integrated luminosity of $3.0,mathrm{fb}^{-1}$ collected by the LHCb experiment. Relative magnitude and phase information is determined, and coherence factors and related observables are computed for both the whole phase space and a restricted region of $100,mathrm{MeV/}c^2$ around the $K^{*}(892)^{pm}$ resonance. Two formulations for the $Kpi$ $S$-wave are used, both of which give a good description of the data. The ratio of branching fractions $mathcal{B}(D^0to K^0_S K^+ pi^-)/mathcal{B}(D^0to K^0_S K^- pi^+)$ is measured to be $0.655pm0.004,(textrm{stat})pm0.006,(textrm{syst})$ over the full phase space and $0.370pm0.003, (textrm{stat})pm0.012,(textrm{syst})$ in the restricted region. A search for $CP$ violation is performed using the amplitude models and no significant effect is found. Predictions from $SU(3)$ flavor symmetry for $K^{*}(892)K$ amplitudes of different charges are compared with the amplitude model results.