Best way to reference a scene object's position to an instantiated object?

I have this code which takes an object from a list of prefabbed object “Enemies” and instantiates them into the scene. On the Enemy’s turn, the enemy runs up to the position of the “Action Space ,” an empty game object, and instantiates a “Projectile” prefab at the same position of some other empty object “Spawn Points.”
The enemy’s turn worked normally when the Enemy was just a normal scene object, but now that I am instantiating the Enemy, it doesn’t keep the transforms of the Action Space & Spawn Points (I referenced their transforms by dragging them onto public transform variables in the Enemy’s script). As far as I know, it is because instantiated prefabs can only refer to other instantiated prefabs and not scene objects because they were designed to be scene independent.
I’ve tried and read a lot on how to give the prefabs these references, but the methods I’ve tried either haven’t worked (e.g, referencing the transforms through another object’s script, even making the Enemy a child of said object) or are very costly to the game. What’s the best and if possible most beginner friendly way to reference a scene object’s transform to an instantiated prefab?
PS: I will send code if needed.

You can store those variables in a separate script, personally I prefer to store them in the GameManager of the scene, and once you spawn your enemies make them get the variables they need from GameManager before doing anything else, GameManager should be a singleton in this case so you can access from the enemy by simply writing:

(Vector3 position, Vector3 position2) = GameManager.Instance.GetSetupValues();

And inside your GameManager you should have something like:

// This GameManager script should be a singleton
[SerializeField] Vector3 _spawnPosition, _bulletPosition;

public (Vector 3 pos, Vector3 pos2) GetSetupValues()
      return (_spawnPosition, _bulletPosition);

And this is what I used to return multiple types in one method:
Tuple types - C# reference - C# | Microsoft Learn
And this is how you can make a singleton:
Singletons in Unity (done right) - Game Dev Beginner