Looks like you are creating a bilayer material (van der Waals heterojunction) here, is that the intention, or did you want an in-plane junction?
Anyway I would rather use the Builder and the Interface Builder there, which is more of a single interface tool, whereas the one you have opted for is more suitable to make multiple interface structures and perhaps try different Miller indices etc, which is not too relevant for you. The Interface Builder has more interactive controls for a specific interface.
The in-plane junction is also easier to make with substitution probably, just make a BN sheet and replace parts of it with C atoms and relax the structure.
