Boundary conditions are defined by the label attached to a boundary object. Multiple boundary objects might have the same label and therefore attached to the same boundary condition. If there are multiple boundaries in a given direction of an element, the one defined first in the configuration, will be used. This allows you to set the precedence order of boundaries that should be used at any intersections.
Only boundary labels that actually appear in the final mesh will be written to the header description of the boundaries in the mesh.