Cannot control gameobject and play animation simultaneously

Hey there! I've been trying to fix this problem for a little under a week now, and have no idea what i'm doing wrong:

I have this turret that you control with the mouse. I want it to play a recoil animation on the nozzles the same time it fires a projectile. However, I can't get this to work. Here are some things that happen.

1. If I had the turret rotated, it would jerk back to the position it was animated in once I fired. And I can't control the turret while firing.

1. when I tried to make a new animation in Unity, It transported the entire turret to 0,0,0. And it didn't animate the nozzle, it animated the entire turret gameobject.

Here is the animation script:

 #pragma strict
 
 var projectile : GameObject;//ignore
 internal var nextFire :float;
 
 var fireRate : float = 0.5;
 
 var clip1 : AnimationClip;
 var clip2 : AnimationClip;
 
 
 function Start () {
 
 
 
 }
 
 function Update () {
    if (Input.GetButton ("Fire1")&& Time.time > nextFire) {
    
       animation.Play(clip1.name);
       animation.Play(clip2.name);
       
       nextFire = Time.time + fireRate;
       
      
       
    }
 }

And the control script(sorry about the mess):

 //#pragma strict
 
 /*var forwardSpeed : float = 3;//ignore
 var roll : float = 2;//ignore
 var lift : float = 25; */
 var yAxis : float = 2;
 var xAxis : float = 2;
 /*var deadZoneXPlus : float = 5;  
 var deadZoneXMinus : float = -5;
 var deadZoneYPlus : float = 5;
 var deadZoneYMinus : float = -5;
 var bullet : GameObject;
 var speed : float; */
 
 function Start() {
 
   
 }
 
 
 function Update () 
 {
   
       //forward speed
   //var forward = Input.GetAxis("Mouse Y")*forwardSpeed;
 
  
    //turn roll
  // var rolly = Input.GetAxis("Mouse X")*roll;
  
     //rotate Buggy
  
    //var lifty = Input.GetAxis("Jump")*lift;
    //Lift dropship
  
     var y = Input.GetAxis("Mouse Y")*yAxis;
   
    
    
      //yaw
     var x = Input.GetAxis("Mouse X")*xAxis;
  
   //roll
   //transform.Rotate(0,rolly, 0);
    //if ( Input.GetAxis ("Mouse X") > deadZoneXPlus || Input.GetAxis("Mouse X") < deadZoneXMinus) 
   //{
   
   //pitch
   transform.Rotate(0,y,0);
   //}
   
   //if (Input.GetAxis ("Mouse Y") > deadZoneYPlus || Input.GetAxis ("Mouse Y") < deadZoneYMinus) {
   //yaw
   transform.Rotate(x,0,0);
   //}
   
   //move forward
   //rigidbody.AddRelativeForce(0,forward,0);
   
   //lift
   //rigidbody.AddRelativeForce(0,0,lifty);
   
   
   /*if (Input.GetButton("fire1")){
   
   var clone : GameObject = Instantiate(bullet, transform.position, transform.rotation);
   
   clone.transform.TransformDirection(Vector3(speed,0,0));
   */
   
     
   
   }
   
 
 }