Accurate modelling atmospheric transport over complex terrain is challenging due to processes interacting with the orography and the use of finite resolution wind fields in Atmospheric Transport Models (ATMs). An unresolved issue is the representation of mountain stations within ATMs, and particularly the choice of model height that best represents mountain observations. This study proposes a methodology to determine optimal heights for representing mountain sites in ATMs, using FLEXPART driven by ECMWF ERA5 wind fields at two spatial resolutions. Three different release height methods were evaluated: i) sampling inlet height (S-rh), ii) an intermediate height based on model orography (P-rh), and iii) a varying release height determined by matching ERA5 potential temperature with observations (T-rh). A sensitivity analysis is presented, determining the optimal particle release height for three mountain sites and its influence on the simulated mixing ratios, using SF₆ as a tracer and two prior fluxes across different seasons and diurnal cycles. Results show that the model performance strongly depends on the release height choice, spatial resolution of the wind fields, station characteristics and atmospheric condition. The varying T-rh, generally provided a good representation of the observations across seasons and sites, although summer advection was not well captured. S-rh systematically underestimated observed variability, leading to a weaker source-receptor relationship (SRR) and biased posterior emissions. These findings highlight the importance of representing mountain stations in ATMs to reduce the model-data mismatch and that an inappropriate release height can lead to systematic bias of posterior flux estimates.