All your managers hired in your regular prisons, as well as the ad shredder bundle, will work during the Alien Invasion. They will apply the same boosters as in your permanent prisons.
However, you will be able to unlock extra items paid by gems: 
Special items paid by gems during the event (SERGEANT, EXTRA BARRACKS, WEAPONS' WORKSHOP AND SIMULATOR) will only be available during the event where they were acquired. You will be able to reduce the training times and earn more money per hour thanks to those features.
Every player will be able to play the voluntary event without spending gems. The event won't affect the normal progress of your permanent prisons.