In Settle3D, an excavation is considered to be a negative load.
If you were to model only the excavation, the loading stress would be -γd where d is the depth of the excavation and γ is the unit weight of the soil. The loading stress when modeling only the excavation is the negative of the overburden stress. The total stress would then be 0 kPa (assuming metric units), since the overburden stress is always added to the loading stress to get the total stress.
If you specify a load of, say, 100 kPa at the bottom of the excavation, the calculated loading stress will be 100 kPa + excavation load = 100 + (-γd). The overburden stress is then added on to make the total stress equal to 100 kPa. Basically, if you want to model a certain loading stress at the bottom of an excavation, you need to specify a stress equal to the stress from the external load as well as the stress from the overburden.