Using a Master Control Script w/Instantiated prefabs & multiple scenes?

I've dabbled in Unity with several mini-projects, and am now attempting something with a little more structure. I'm realizing that I don't know the best way to set up a Master Control script that will work with instantiated objects and in multiple scenes.

My project has two scenes - one which is an empty game map, and another which is a warehouse where my prefabs live.

My game has turret towers which the player can place (instantiate as prefabs) around the map. Each of these towers has a script for tracking the mouse and firing at a target/clicked object.

I'm using a master control script assigned to a dummy object in the scene to handle the raycast for targeting, as well as a boolean which toggles whether turrets should be firing or not. This is also where I'll later track things like game states or score, etc. This seems like a good idea for performance and organizational reasons.

The turrets have their own script, with a variable which points at the Master Control script. This works great if I pre-place the turret in my scene and manually point that variable at a dummy with the MC Script on it. When I try to make this systemic, however, I run into two problems:

1) I don't know where Master Control Script should actually live. As mentioned: I have it currently on a dummy object in the scene, and that script includes DontDestroyOnLoad(transform.gameObject); in the Awake() function, but I'm not sure this actually allows me to have one script which will persist across all scenes. Right now I have to pre-place my turrets in each scene, as well as place a dummy with the MCS in each scene (and point each turret script to that dummy).

2) Probably related to the above, I cannot assign the variable on my turret prefab to point at the object with the MCS.

I think this boils down to me not quite understanding the best way to use prefabs. Would love to hear some input on how to best structure things.