Is it obligatory to dispose of the excess amount over what is ostensibly deserved from a bonus, or is it permissible to keep the full amount, taking into consideration that the manager granted the amount under his authority and does not know the extent of the company owners' approval of the details?

If the manager is authorized by the company owners to grant the bonus, then there is no blame upon you in taking it in full. However, if he is not authorized and gave you more than you deserve out of favoritism, then you must return the excess to its rightful owners (the company owners), and it is not permissible for you to give it away as charity.