Question

Why does the electron config for (a random example) Fe #+ beome [Ar] 3d^5 instead of [Ar] 4s^2 3d^3? Why and when do we transfer these two electrons to the 3d orbital?

Answer 1

Each orbital can hold a maximum of two electrons, so the maximum number of electrons you can put into the subshells are 2 in the s-orbital, 6, in the p-orbital, and 10, in the d-orbital (14 in f-subshell). This is going into quantum chemistry, in which it relates to energy levels between orbitals.
Just keep in mind that d-orbitals are lower in energy than p-orbitals, which is why electrons would prefer to be filled there first.

keep in mind that by pauli exclusion principle, you cannot fit more than 2 electrons in a same space, cloud, or whatver it is they call it in chemistry text books.