How do I add a customer number/Preferred number along with the company Billing Account Number? 

Add the preferred number in the ID field and then add the Billing Account number in the booking as normal at the same time. If completed at the same time, the customer number will not override the billing account. However, if the customer number is added after the reservation is made, the voucher will need to be re-issued to avoid the customer having to pay on credit card.