Depending on what you mean by complex structures. If this corresponds to a unit cell of bulk material with many atoms, and you want to calculate transmission spectrum of this perfect (without scatters) material, you may stick to bulk configuration as suggested in the first tutorial you have mentioned.
If you want to calculate the electron transmission through a non-perfect structure such as a structure with a defect or just interface structure between two different materials attached to two electrodes, which can often be assumed to be made of the same kind of materials (but perfect without defects or other scatters), you should then use device configuration as stated in the ATK Transport tutorial.
