Thin layers of topological insulator materials are quasi-two-dimensional systems featuring a complex interplay between quantum confinement and topological band structure. To understand the role of the spatial distribution of carriers in electrical transport, we study the Josephson effect, magnetotransport, and weak anti-localization in bottom-gated thin Bi$_2$Te$_3$ topological insulator films.We compare the experimental carrier densities to a model based on the solutions of the self-consistent Schrodinger-Poisson equations and find excellent agreement. The modeling allows for a quantitative interpretation of the weak antilocalization correction to the conduction and of the critical current of Josephson junctions with weak links made from such films without any ad hoc assumptions.