Particle transport in fluid flows is of broad relevance due to its ubiquity in natural, industrial, and biomedical systems. When particles are soft, particle-tracking becomes significantly more complex. Such particles (including capsules, droplets, vesicles, hydrogels, and biological cells) exhibit deformation-driven transport and deposition behavior that differs fundamentally from that of rigid particles. However, their dynamics, especially in large ensembles and complex flows, remain poorly understood. In this work, we study the dynamics of soft particles suspended in viscous flows using our novel and efficient point-particle pseudo-rigid body framework, (Wedel et al. 2024, Wedel et al. 2025, Wedel et al. 2026). The method resolves particle barycenter and shape dynamics without requiring particle discretization, thereby enabling simulations of $\mathcal{O}(10^5–10^6)$ particles at low computational cost while supporting general material behavior. The framework is first validated against relevant benchmark cases, showing good agreement for both initially spherical and non-spherical soft particles. The approach is then applied to particle transport and deposition in a complex macroscopic flow field, specifically a human nasal cavity under steady inhalation conditions. We find that deposition patterns are primarily governed by particle size and inertia, with smaller particles penetrating deeper and larger particles depositing preferentially in the anterior region. Particle deformability and initial stress-free shape significantly affect deposition statistics for small particles, whereas these effects diminish for larger particles as trajectories become increasingly ballistic. Substantial deformation upon deposition is observed for soft, initially elongated particles, suggesting that interaction of local flow-related high shear regions and soft particles may be relevant for intranasal drug delivery. Overall, this study highlights the importance of particle deformability in predicting soft-particle transport in physiologically and technologically relevant flows. The proposed framework bridges the gap between interface-resolved simulations and large-scale particle transport models, providing a scalable tool for applications ranging from aerosol drug delivery to soft matter suspensions.