To unlock doors you must put the right amount of the correct runes in. You are told what the solutions in the pedestal book "Magical Runes for Dummies" in the room. You pull levers to highlight runes. When you have the correct solution runes highlighted the relevant door is unlocked.
There is a corpse to loot who has a note that will hint about security, and there is a missing page from the book in the facility. When you have that page in your inventor and re-read the "Magical Runes for Dummies" on the altar you will get the final solutions for the doors.
Getting a pen & paper out and making a list of known runes, solutions, and which levers highlight which runes, will help.