The boundary faces are the Triangles. To locate a boundary condition, you can put the same reference on a set of triangles. This reference will be unchanged by Mmg3d .
You can put every integer. However the new vertex created by Mmg3d will have a reference number equal to zero. Be careful, if there are several reference numbers for tetrahedra, Mmg3d will consider several subdomains.
No, you can give only the tetrahedra.