$params['product']=$productid;
$params['super_group'] = array( $simpleid=> $qty );
$cart = Mage::getModel('checkout/cart'); //Get cart object
$cart->init();
$cart->addProduct($productid, $params);
$cart->save();

$cartHelper = Mage::helper('checkout/cart');
$cartHelper->getCart()->removeItem($simpleproductcartid)->save();

$cartHelper->getCart()->updateItem($somecartrowid, $params)->save();

{"name":"Amigne 2012", "type":"grouped", "parent_id":"635", "entity_id":"567", "qty":3}

"567":{"cartid":"1000","qty":3},

$cart->updateItem('1000',1)

{"name":"Amigne 2012", "type":"simple", "parent_id":"", "entity_id":"567", "qty":1}

"567":{"cartid":"1002","qty":1}

public function updateItem($itemId, $buyRequest, $params = null)
     * @param int $itemId
     * @param Varien_Object $buyRequest
     * @param null|array|Varien_Object $params
     * @return Mage_Sales_Model_Quote_Item

public function addParamsToBuyRequest($buyRequest, $params)
     * $params holds parameters of what operation must be performed:
     * - 'current_config', Varien_Object or array - current buyRequest that configures product in this item,
     *   used to restore currently attached files
     * - 'files_prefix': string[a-z0-9_] - prefix that was added at frontend to names of file inputs,
     *   so they won't intersect with other submitted options
     *
     * @param Varien_Object|array $buyRequest
     * @param Varien_Object|array $params
     * @return Varien_Object

$cartdata[988][qty]=100
$cartdata[999][qty]=1
$cartdata[1001][qty]=1