How do you change a players position during an animation?

Hello, I've come across a problem recently. I'm making a endless runner. In my running animation i want him to go up and down so in my animation i used the move tool to make him go up in a part of the animation. But when i do that it of course messes up the game and my guy wont move. I believe this happens because the animator is interfering with the player controller when you move the position of the player. Someone had a similar problem and suggested making an empty parent object and putting the player controller on that. But that wont work because I think my script needs to find my players collider and rigid body. If anyone could tell me a solution to this problem by telling me how i could modify my script when its on the players parent object to make it work or another solution it would be greatly appreciated. Here is my script:

public class PlayerController : MonoBehaviour

{ public float movespeed;

public float jumpforce;

private Rigidbody2D myRigidbody;

public bool grounded;

public LayerMask whatIsGround;

private Collider2D myCollider;

private Animator myAnimator;

// Use this for initialization

void Start() { myRigidbody = GetComponent(); myCollider = GetComponent(); myAnimator = GetComponent(); } // Update is called once per frame

void Update()

{

grounded = Physics2D.IsTouchingLayers(myCollider, whatIsGround);

myRigidbody.velocity = new Vector2(movespeed, myRigidbody.velocity.y);

if (CrossPlatformInputManager.GetButtonDown("jump") || Input.GetMouseButtonDown(0)) {

if (grounded)

{ myRigidbody.velocity = new Vector2(myRigidbody.velocity.x, jumpforce);

} }

myAnimator.SetFloat ("Speed", myRigidbody.velocity.x);

myAnimator.SetBool ("Grounded", grounded);

}

}

Thank you for your help.