Dear Chris,
Ultimately, it shouldn't matter. If the SCF goes well, you should arrive at the correct ground state regardless of the initial shell population (as long as it is neutral). The atomic configuration (neutral atoms or ions, see MgO input example in https://tutorials.crystalsolutions.eu/tutorial.html?td=barebone&tf=basic_tutorials#bs) in the initial SCF guess (default choice: density matrix as superposition of atomic densities) is defined by the atomic shells population.
And yes, with ATOMSPIN you set the initial spin on a specific atom (take care about symmetry and atoms that are translationally related) to set the starting point for the SCF.
If the SCF goes well, when you do the corresponding population analysis (say Mulliken), you should be able to distinguish the different "oxidation" states of different oxygen atoms and locate the unpaired electrons. I have done so with systems containing Cu1+ and Cu2+ in the lattice and this has worked beautifully (within the same basis set).
If you have a specific INPUT file in mind, you can upload it for cross-checking.
Cheers,
Aleks

