@Laura you need to create inter company customer and vendor for each sub vice versa. make sure to define the "represent subsidiary" field for both vendor and customer so the transactions will be tagged as intercompany transactions. This will allow you to bill and receive payment subsidiaries, you can always use intercompany JE to move funds but to have a proper business process intercompany billing is the best practice. More on this suiteanswers#20804.
Scenario Company B is doing a project for their customer, and Company A procured something for the project and paid the vendor, now Company A (Vendor of B) will send vendor invoices to Company B (customer of A) for payment. Comp B will pay Comp A and tag the cost to their project. There can be many more scenarios.