Which structures of an atom take part in a chemical bond

For cyclohexane compounds drawn in a chair conformation:   -axial bonds are vertical  -equatorial bonds are parallel to two bonds within the ring.  thus, as i assume the chair conformation is drawn:   -the x group is in an axial position, as are the five other vertical bonds.  -three axial bonds are on the top face of the ring  -the other three axial bonds are on the bottom face  the position of the second substituent on each ring carbon is equatorial.  gauche groups must be on an adjacent carbon such as carbon 6 and carbon 2, and also gauche groups are rotated by 60 degrees relative to each other.  drawing the newman projections for c1–c2 and c1–c6 aids in visualizing the groups that are gauche to the y group on c1.  click this link and watch some academic videos that may you more understand the topic 

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.