What is the ruling of Islamic law on an employee using the internet, phone, and printouts belonging to the workplace for personal use, and how can he atone for that without the knowledge of the institution's manager?

You must do one of two things: either seek the school owner's forgiveness for the money he incurred as a result of your using these items for non-work purposes, or return that money to him, even indirectly, while striving to estimate it if you cannot determine the exact amount. It is not permissible to merely return the printed materials to the school library without his consent, as his silence does not mean he relinquishes his right or gives his consent.