populate 2d array with existing grid of gameobjects

From my understanding I'm assuming you want to make a 2D array containing your cubes. One simple way is making a serialized field that will have it's references specified in the editor. But since the editor can't serialize a 2D array, an alternative option is to make a custom class, put an array there and then make an array of those class instances.

Here's a quick example:

 using UnityEngine;
 
 public class TestScript : MonoBehaviour
 {
     public CollectionOfCubes[] cubes = new CollectionOfCubes[0];
 
     private void Start()
     {
         for (int i = 0; i < cubes.Length; i++)
         {
             for (int j = 0; j < cubes[i].instances.Length; j++)
             {
                 GameObject currentCube = cubes[i].instances[j];
                 Debug.Log($"Cube name: {currentCube.name}");
             }
         }
     }
 }
 
 [System.Serializable]
 public class CollectionOfCubes
 {
     public GameObject[] instances = new GameObject[0];
 }

If you want to write a better solution, maybe something that doesn't require dragging the cube references by hand, you can check out some of the following references:
https://docs.unity3d.com/ScriptReference/Transform.GetChild.html
https://docs.unity3d.com/ScriptReference/Component.GetComponentsInChildren.html
https://docs.unity3d.com/ScriptReference/Object.FindObjectOfType.html

@Quickz Thank you so much, that's really helpful. I was thinking of assigning them explicitly to the 2D array as there are not too many of them, but I like your idea much better!