For incompressible (constant density) flow the reference pressure is relative pressure or gauge pressure. Therefore zero is equivalent to atmospheric pressure. The relationship between gas density, pressure, and temperature is only relevant for compressible flow, usually through the ideal gas equation.

For incompressible heat transfer Caedium uses the Boussinesq approximation, which assumes negligible density variation.

All boundary conditions in an incompressible simulation use relative pressure. Typically you would set the outlet pressure to be your reference pressure (as it is by default) and then set the inlet pressure explicitly if you know the pressure drop across the system. Imposing an inlet pressure instead of an inlet velocity (default) can lead to less robust simulations that take a long time to converge.