If you take out this line of code from the shipping.php...

Code:
if ($shipping_weight > SHIPPING_MAX_WEIGHT) { // Split into many boxes
      $shipping_num_boxes = ceil($shipping_weight/SHIPPING_MAX_WEIGHT);
      $shipping_weight = $shipping_weight/$shipping_num_boxes;
      }
It can work for adjusting for different package sizes... but only 2. This works only if you always send in one package.