Does this do what you're looking for?

var projectile:Transform;
var shootSpawn:Transform;
var clipsLeft:int = 10;  // how many clips the player has
var clipSize:int = 6;    // how many bullets in 1 clip
private var ammo:int;    // how many bullets left in the current clip

function Start() {
    ammo = clipSize; // Start with this many bullets.
}

function Update() {
    if(Input.GetButtonDown("Fire1")) {
        if(ammo > 0) {
            var clone:Transform = Instantiate(projectile, shootSpawn.position, shootSpawn.rotation);
            Physics.IgnoreCollision(clone.collider, collider);
            ammo--;  // Subtract 1 bullet
            if(ammo <= 0)
                Reload(); // Do you want to call reload here...
        }
        else {
            Reload(); // ...or here?
        }
    }
}

function Reload() {
    if(clipsLeft > 0) {
        clipsLeft--;
        ammo = clipSize;
        // Play sound/animation ?
    }
    else {
        // No more clips left...
    }
}