When it is inter-company, I have been exposed to below flow. I am sure there can be different other scenarios too.

A- After delivering the Internal CO, you can Invoice it. Then RMB on the header of the Invoice and do Send Invoice. 

(you should define INVOIC in Message setup for both Internal customer and Supplier, additionally, don’t forget to define SUPPEXT as below)

B- Now you will receive an incoming message which you can find in window; Multi-company External Supplier Invoices. (you can search by the Internal CO Invoice no)

C- RMB on the line: Check Invoices > Create Invoices 

D- If there are any Errors, view in Error Log

Documentation on http://docweb.corpnet.ifsworld.com/ifsdoc/Apps10/Documentation/en/default.htm?openpage=http://docweb.corpnet.ifsworld.com/ifsdoc/Apps10/Documentation/en/Invoic/tbwExternalIncInvoiceHead.htm would also help you. 

E- After that, invoice the External CO as well.