В файле catalog/model/extension/shipping/pickup.php
$quote_data['pickup'] = array(
'code' => 'pickup.pickup',
'title' => $this->language->get('text_description'),
'cost' => 0.00,
'tax_class_id' => 0,
'text' => $this->currency->format(0.00, $this->session->data['currency'])
);
замените на
$cost = $this->cart->getSubTotal() - ($this->cart->getSubTotal() * 0.9);
$quote_data['pickup'] = array(
'code' => 'pickup.pickup',
'title' => $this->language->get('text_description'),
'cost' => -$cost,
'tax_class_id' => $this->config->get('total_shipping_tax_class_id'),
'text' => '( - ' . $this->currency->format($cost, $this->session->data['currency']) . ')',
);
0,9 - это и есть 10% скидки.