Transportation costs in Navigator are derived using reference data that are market estimates and intended to be adjusted up and down by adjusting the discount factor relative to your model. The Transport table can be accessed by selecting CONFIGURATION within the Model Manager. See here for more details.
The discount factor is by default set to "1". Changing it will result in all of the costs in the model for a respective mode of transportation being multiplied by a factor of "x" (where x is the discount factor). Thus, if you wanted to capture a 40% discount rate you might receive on all "Ground Parcel" transportation, then you would change the discount factor for "Ground Parcel" to ".6".
In addition, you can set a "Minimum Shipment Cost" for a respective mode in this table. See here for more details.