We are a bakery with wholesale customers, too! We use the House Accounts feature to manage these customers. While there is no online solution right now, you could allow customers to enter their orders online and leave the orders unpaid. Your staff can then apply the appropriate discount at the POS when they accept the order, and charge the order to their account.
In our case, we have a standard wholesale discount and our customers have standing orders, so they do not place orders for each delivery.
