When two oxygen atoms bind to a carbon atom what happens to the other 4 electrons? Are these what are converted into energy and emitted?
The electrons are not lost/emitted.
When two atoms bond, they share their electrons.
Let's take a simpler molecule: H2O.
Each H by itself has 1 electron existing somewhere around it.
O by itself has 2 electrons existing somewhere around it.
In the H2O molecules, the electrons are shared, so basically:
Each H in H2O has 2 electrons existing somewhere around it (its original electron, and one electron from O)
And the O in H2O has 4 electrons existing somewhere around it (its original 2 electrons, and one electron from each of the two H)
If I broke apart this molecule would it be because I introduced enough energy for one of the atoms to have its full set of electrons and nullify the electro magnetic imbalance?
No, there is no electro-magnetic imbalance.
That "shared electron" configuration is at a lower energy state than each atom having a separate electrons.
When you introduce energy, you give the atoms enough energy to switch to the higher energy state.
When the opposite happens and two free atoms bond together, they switch to a lower energy state, so energy is released in the form of photons, heat, radiation, or whatever else.