You would need to find this section of code in the United Parcel Service ups shipping module:
And customize what is used in place of:
$methods = array('id' => $type,
'title' => $this->types[$type],
'cost' => ($cost + MODULE_SHIPPING_UPS_HANDLING) * $shipping_num_boxes);
When the $type is the same as the code(s) ... see codes in module ... match your customized handling charges ...
NOTE: shipping modules are NOT overrideable, however, you can clone them so that your custom module does not get overwritten with each upgrade ...