How can I understand the Lewis acid-base interaction of iron(III) and water?
So, effectively, the question is: How are electrons from the covalent bond between ligand and central metal atom or ion placed with regard to the electron configuration? 

$\ce{Fe^{3+}}$ has the condensed electron configuration of [Ar]$3d^5$. When the ligands approach the iron ion from the X, Y, and Z, the ion forms six bonds. It would be incorrect to state that the remaining 3d electrons are involved in the bonding with the ligands. Instead, the iron ion uses 6 orbitals from the 4s, 4p, and 4d orbitals to accept the lone pairs of electrons from the ligands. However, before they are used, the orbitals are hybridized in order to create six orbitals of equal energy. 

If you want to dig deeper into the subject, I highly recommend the lecture notes from this webpage here.