To select "Bill To Company" just type an existing contact, like you would type an existing customer, and select it.
Bill To Company will be always a different contact, from the customer.
If the Customer is the Bill to contact, just leave it blank, you don't have to select it twice.
We can give you 2 examples of what features are associated:
1. Somebody else will pay you for the delivery.
For instance, a dealership gives you a customer who wants to transport a vehicle and will pay for the transportation.
In this case, you will communicate about everything with the customer, schedule pickup, etc.
The customer will be in the customer section.
However, the invoice should be sent to the dealership. The dealership will be in the Bill To Section.
The dealership will appear on the invoice: 
2. The dealership gives you customers and wants to keep track of these shipments for payment / other purposes.
Bill to have access to the Customer Portal and can log in with this page - https://www.carshipio.com/Public/OrderStatus/
We will show all the orders where this Dealership is assigned as a customer or Bill To Company.
Abc Dealership sent you 3 orders for John, 2 for Vicky, and 4 orders they are customers.
On the portal, in my orders section, they will see all the orders above.
Here is more info about the customer portal - Customer portal