The Abilities for the brain give you two choices and both are meant to be used against Psionic attacks. Some soldier types will benefit far more than others from these upgrades, but Snipers and Assault seem to get the most from Gene Modification.
It would make sense to do one upgrade at a time in order to keep your soldiers in rotation for the difficult missions. There is no time discount for doing them all at once. Just like the abilities your soldiers gain through advancement, they will only be able to take one upgrade per area. The soldier can have their Brain, Eyes, Chest, Skin, and Legs upgraded.
