BEAVA is not a program for "generating the model" if by that you mean generating the geometry, property, supports, etc.
BEAVA is solely for arriving at critical load magnitudes and their positions on the structure due to vehicle (moving) loads. It arrives at these critical loads by using the influence line method for members and influence surface method for plate elements.
So, the sequence of operations is :
Enter the modeling mode of the STAAD.Pro GUI.
Generate the geometry, properties, supports, etc.
Assign the loads due to gravity, wind, seismic, temperature, snow, etc.
Save the model and keep a copy of it to guard against a crash and potential loss of data.
From the modeling mode of the STAAD GUI, enter the BEAVA module. So, BEAVA now has all the basic data necessary for the influence line and influence surface generation. Choose the vehicle and generate the critical loads. When you exit BEAVA, those generated loads (in the form of joint loads, member and element pressure loads) will then get written into the STAAD model. You are now back in the modeling mode of the STAAD GUI.
Assign the remainder of the data, if any, such as the load combinations, command for the type of analysis, design parameters and commands, etc.
Thus, you'll have a single model with all the loads - vertical and transverse.
Run the analysis and view the results. Those results will presented be for all the loads in the model.
So, there is no need for a separate model for just transverse analysis.