The two sponges will be differing densities.... theory being, the looser one (more air holes !) will house the bacteria and the finer one will stop the smaller particles from re-entering the tank.
Point is, have the bacteria actually read the theory/manual ? Of course not, they will setup home everywhere (if they are allowed) so its all a bit of a gimmick, best you can hope for is that the coarser foam traps the big particals, and prevents the finer sponge from clogging so quickly !
So in short, NO it makes no difference to the cycle.