The central regions of disc galaxies host a rich variety of stellar structures: nuclear discs, bars, bulges, and boxy-peanut bulges. These components are often difficult to disentangle, both photometrically and kinematically, particularly in star-forming galaxies where dust obscuration and complex stellar motions complicate interpretation. In this work, we used data from the GECKOS-MUSE survey to investigate the impact of dust on axisymmetric Jeans Anisotropic Multi-Gaussian Expansion (JAM) models and assess their ability to recover kinematic structures in edge-on disc galaxies. We constructed JAM models for a sample of seven edge-on (i ⪆ 85°) galaxies that span a range of star formation rates, dust content, and kinematic complexity. We find that when dust is appropriately masked, the disc regions of each galaxy are fit to χreduced2 ≤ 5. We analysed 2D residual velocity fields to identify signatures of non-axisymmetric structure. We find that derived dynamical masses are constant within 10% for each galaxy across all dust masking levels. In NGC 3957, a barred boxy galaxy in our sample, we identified velocity residuals that persist even under aggressive dust masking, aligned with bar orbits and supported by photometric bar signatures. We extended this analysis to reveal a bar in IC 1711 and a possible side-on bar in NGC 0522. Our results highlight both the capabilities and limitations of JAM in dusty, edge-on systems and attempt to link residual velocities to known non-axisymmetric kinematic structure.