Character Controller and Navmesh Agent

Hey guys I was needing help, I was working in an older version of unity and it was working fine, then when I updated to the latest version of unity it broke my third person character, when I try using navmesh. Like when I try to jump either the character doesn’t jump or the character just flies forever. From what I have looked online I need to disable the navmesh when I am trying to do the jumping but I cant figure out where to put the code for doing that. Or even what to do to fix the problem, Cause I was wanting Navmesh so i could better make the barriers in my game, But if I can’t jump whats the point, any help or leads into what to do to make it work out would be greatly appreciated. Thanks in advance.

Sorry if it was confusing to anyone. But I found the answer to what I was asking, It was the navmesh trying to update the position and that was disabling the jumping that the controller was giving in order to fix that, you have to make a new script and add this to it.
using UnityEngine;
using System.Collections;

public class NavAgentPatch : MonoBehaviour {
	public NavMeshAgent agent { get; private set; }
	// Use this for initialization
	void Start () {
		agent = GetComponentInChildren<NavMeshAgent>();

		agent.updatePosition = false;
		agent.updateRotation = false;
	}

}

and then you have to have both enabled which will re-allow the jumping and everything. Hope this helps anyone who has this problem.