If logos are displayed in a BikeCAD model, they should appear just the same in the model exported to FreeCAD. For a clearer display, they will each have a thickness associated with them which is defined in the Export to FreeCAD dialog box. Logo number 2 will by default have a greater thickness so that it will appear over top of Logo number 1.
One logo that is treated differently is the head tube logo. In BikeCAD it is common to apply some amount of offset to the logo so that it appears to be displayed on the front of the tube. Just before exporting such a model to FreeCAD, this offset should be set to zero, so the logo displays on the side of the tube. When the model is exported to FreeCAD, the logo will automatically be rotated around the head tube so that it will appear on the front of the tube in the FreeCAD model.