How can scientists study the inner structure of the atom

The number of protons, neutrons, and electrons in an atom can be determined from a set of simple rules. The number of protons in the nucleus of the atom is equal to the atomic number (z) The number of electrons in a neutral atom is equal to the number of protons,

The problem here is that according to aufbau principle before 3d orbital 4s subshell comes.after filling 3p orbital with electrons you have 4 electrons left, you place two in 4s with opposite spin and the other two in 3d in any of its two orbitals of total five orbitals with the same spin.