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trouble with reconciling transactions that have two invoices

I am going to brace for the fact that we will have to talk about this possibly.  It is going to be difficult to fully capture what I am going to tell you.  I am trying to reconcile the orders so I can run the report to send with my billing.  We have an order where part of the order is being shipped from the manufacturer and will be billed on a separate invoice but with the same requisition number.  The requistion number is ITQA17-RRRW-GYS-2001. So I need to bill for what has been delivered.  I cannot reconcile this invoice yet since everything has not been received but I need to pay for what has been received.  So I won't be able to run a report that will show everything.  Is there a way others have dealt with this?  Is there a way to have a status of partially reconciled and have a way to split payments so we can list more than one invoice number?  Help!!!
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