In order to bill the shipping charges to another account, you would need to specify who to bill the shipping charges to while creating your shipment.
To do so, create a shipment as you normally would.
When you arrive to the Services page (the page that shows you all service levels and prices) there is a section at the top right called Show Details.
If you click there, you will be able to see the details of your shipment including 2 buttons. Enable the one under Duties and Taxes so that it moves towards My Account. Continue through all the steps until the label is generated.
Note: You cannot currently bill the shipping charges to another Secureship account.