If you go to http://physics.rutgers.edu/pythtb/examples.html the second example is graphene with a two-atoms unit cell. Basically you want to keep it the same, but add more sites with this command

my_model.set_hop(t, o0, of, [ i0, i1])

where o0 and oF are the initial and final orbital index, and i0 and i1 are the unit cell index. If you need more information be more concrete on what you had tried.