Generally by using the dimensions and heat conduction properties of the exterior surfaces of the house (area of foundations, walls, windows, roof), taking into account the heat gain due to sun, with some local fudge factors applied (loss due to wind, natural ventilation, outside temperature).
Then, after the building is actually built and inhabitated, the calculations are adjusted by the actual energy consumption over year).
As pointed out, competent HVAC companies should have people on staff comfortable with such calculations. However, my experience shows that it is not universally true, and many are just guided by intuition/experience with other projects (i.e. the roof insulation thickness on the previous project was X, so that's good enough for you, or "well, on average we recommend 50W/m2 of heating power when selecting a heat source"). Which probably works fine for many cases (e.g. renovating an older building, where even if the material properties when they were new are known, you can only guess the values after 20 years of service).
Then, after the building is actually built and inhabitated, the calculations are adjusted by the actual energy consumption over year).
As pointed out, competent HVAC companies should have people on staff comfortable with such calculations. However, my experience shows that it is not universally true, and many are just guided by intuition/experience with other projects (i.e. the roof insulation thickness on the previous project was X, so that's good enough for you, or "well, on average we recommend 50W/m2 of heating power when selecting a heat source"). Which probably works fine for many cases (e.g. renovating an older building, where even if the material properties when they were new are known, you can only guess the values after 20 years of service).