Is working with a friend who is a partner to his manager in the latter's company, and who assigns projects to the joint venture, considered haram (forbidden), especially since the owner of the company is unaware of the partnership?

The problem with the aforementioned method is that the partner would be responsible for awarding projects to their own company, which is akin to an agent buying from himself. This is not permissible except with the permission of the principal, because the agent is suspect when buying for himself. Scholars have differed on the ruling of an agent buying for his principal from his own personal money, and the default is impermissibility unless the principal gives permission, because then the liabilities might merge and the suspicion would be removed. Therefore, the company owner must be informed of the true situation. If he permits it, then it is permissible; otherwise, it is not permissible for your partner to award projects to your private company.