I'm not sure I understand what you mean but I think there's only one surface per boundary unless "interior" boundary is a second one.
I made a cube in Design Modeler, marked surfaces as inlet, outlet, top, bottom and walls. It shows 1 Part, 1 Body named Domain. I made a mesh with CFX without changing or renaming boudaries, and then configured on Fluent as follows:
inlet: velocity-inlet. Open Channel Wave BC ticked, Al defaults in Momentum tab, in Multiphase tab Free Surface=0, Bottom Level=5.6, Fifth Order Stokes Waves, Wave Height=1.73, Wave Length=20. I ran command define, then o-c-w-s and check passed.
outlet: pressure-outlet, Momentum: defaults, Multiphase Free Surface=0, Bottom Level=5.6.
top: pressure-outlet, Momentum: defaults, Multiphase Free Surface=0, Bottom Level=5.6.
walls: wall: defaults
I also have a bounday "interior-domain" that I didn't create and it's marked as interior.
Maybe the "interior-domain" could be a second boundary on each surface? How can I remove it if that's the case?