Is there a way to get NetSuite to use an existing authorization if not submitted thru the original record that received the credit card authorization. 

Here is the situation.  We always authorize the card to verify funds are available and all data associated with the card is valid.  Most of the time, we will directly bill from the sales order that received the authorization once the item is shipped, thereby just settling that authorization.  But we also have custom orders where we require the customer to pay before the item ships.  We need to collect a deposit equal to the sales order and authorization amount but it can't be generated as a cash sale because the revenue needs to be recognized once the item ships.