Problems with AI Spawning

So everything works script wise, but when i run the game the NPC wont patrol to the waypoint to get destroyed, it wotn do this because i have the NPC var in editor set to an NPC Prefab, when the prefab spawns on the spawner, it stays still because the Waypoint for the WayPointAI script isn’t it isn’t set because when i cant set the public var for the waypoint that it walks to in the prefabs. and i cant set it the waypoint (in the hierarchy) to the waypoint var on the WayPointAI script attached to the NPC prefab

TLDR: how do i set a public variable on a prefab to an object in the hierarchy?

Spawner script:

using UnityEngine;
using System.Collections;

public class Spawner : MonoBehaviour 
{

	public Transform spawnPoint;
	public Transform spawnObject;
	public int spawnTotal;
		public float timeBetweenSpawns;
	// Use this for initialization
	void Start () 
	{
		StartCoroutine (SpawnGameObject());
	}
	
	// Update is called once per frame
	void Update () 
	{
	
	}
	IEnumerator SpawnGameObject ()
	{
		for( var x = 0; x < spawnTotal; x++)
	    {
			Instantiate(spawnObject, spawnPoint.position, spawnPoint.rotation);
			yield return new WaitForSeconds(timeBetweenSpawns);
		}
	}
}

WayPointAI script:

using UnityEngine;
using System.Collections;

public class Spawner : MonoBehaviour 
{

	public Transform spawnPoint;
	public Transform spawnObject;
	public int spawnTotal;
		public float timeBetweenSpawns;
	// Use this for initialization
	void Start () 
	{
		StartCoroutine (SpawnGameObject());
	}
	
	// Update is called once per frame
	void Update () 
	{
	
	}
	IEnumerator SpawnGameObject ()
	{
		for( var x = 0; x < spawnTotal; x++)
	    {
			Instantiate(spawnObject, spawnPoint.position, spawnPoint.rotation);
			yield return new WaitForSeconds(timeBetweenSpawns);
		}
	}
}

NPCDestroyer script:

using UnityEngine;
using System.Collections;
//public GameObject NPC;
public class NPCDestroyer : MonoBehaviour 
{

	void OnTriggerEnter(Collider collider)
	{

			Destroy(this.gameObject);

	}
}

i reaslized that even if i solved this problem i would have issues elsewhere, i solved this by making it so at the last waypoint of WayPointAI, the NPC would get destroyed