We discuss the dynamics of a condensate in a miniaturized electromagnetic trap formed above a microstructured substrate. Recent experiments have found that trap life times get reduced when approaching the substrate because atoms couple to thermally excited near fields. The data agree quantitatively with our theory [Appl. Phys. B 69 (1999) 379]. We focus on the decoherence of a quantum degenerate gas in a quasi one-dimensional trap. Monte Carlo simulations indicate that atom interactions reduce the condensate decoherence rate. This is explained by a simple theory in terms of the suppression of long-wavelength excitations. We present preliminary simulation results for the adiabatic generation of dark solitons.