in the WA_eCart/scripts/copyShipping.js file, there are two arrays created. One contains all of the frm elements in the builling section of the form:
var billingFields = new Array('firstname', 'lastname', 'email', 'phone', 'fax', 'street1', 'street2', 'city', 'state_province', 'postcode', 'country');
the other contains the corresponding shipping form elements:
var shippingFields = new Array('shipping_firstname', 'shipping_lastname', 'shipping_email', 'shipping_phone', 'shipping_fax', 'shipping_street1', 'shipping_street2', 'shipping_city', 'shipping_state_province', 'shipping_postcode', 'shipping_country');
you need to add your new fields to the list:
var billingFields = new Array('firstname', 'lastname', 'email', 'phone', 'fax', 'street1', 'street2', 'city', 'state_province', 'postcode', 'country', 'newBilling1', 'newBilling2');
var shippingFields = new Array('shipping_firstname', 'shipping_lastname', 'shipping_email', 'shipping_phone', 'shipping_fax', 'shipping_street1', 'shipping_street2', 'shipping_city', 'shipping_state_province', 'shipping_postcode', 'shipping_country', 'newSshipping1', 'newShipping2');