Let's say the customer has to be part of customers_group_pricing 3 ...
You can customize the file:
/includes/modules/order_total/ot_loworderfee.php
Code:
// only show if customer is a member of customers_group_pricing 3
global $db;
$chk_group = $db->Execute("select customers_group_pricing from " . TABLE_CUSTOMERS . " where customers_id = '" . (int)$_SESSION['customer_id'] . "'");
if ($chk_group->fields['customers_group_pricing'] == 3 && MODULE_ORDER_TOTAL_LOWORDERFEE_LOW_ORDER_FEE == 'true') {
switch (MODULE_ORDER_TOTAL_LOWORDERFEE_DESTINATION) {