John,
I am not sure based on your description, but it sound like standard GP features will handle these needs.
Co A (Customer) orders Items from Co B (Seller)
Co B (Seller) Enters Order in GP Sale Transaction Entry then
Clicks on DS (Drop Ship) check box for any line items ordered from Co C (Vendor) then
Clicks on Actions > Purchase to create a Purchase Order for required items
Co B (Seller) sends a Purchase Order to Co C (Vendor)
Co C (Vendor) ships the goods directly to Co A (Customer)
Co C (Vendor) Notifies Co B (Seller) of Shipment to Co A (Customer)
Co B (Seller) Confirms Shipment/Fulfills Order with Shipment Notification Tool
Co C (Vendor) Sends Invoice to Co B (Seller)
Co B (Seller) Enters/Matches Invoice
Co B (Seller) does not do receipts because the Co A (Customer) receives shipment
Co B (Seller) Sends Invoice to Co A (Customer)
Co A (Customer) makes payment to Co B (Seller)
All of these features are available in the Dynamics GP Starter Pack