The main goal in this type of situation is to find an organizational structure that both parties can agree on for the duration of the collaboration. Communication is the most important factor for such a task to be successful. The type of structure that best fits this scenario is a matrix organization.
Matrix organization allows for multiple functional and project managers to be present from both companies. This ensures that the goals and interests of both companies are recognized and met. This indirectly creates a system of checks and balances where one company’s interests do not over power the others. Functional and project-based organizations typically leave one person in charge. This tends to disrupt the balance and would create a one sided collaboration.