How can one dispose of money gained from illicit work performed outside the official scope of the company and without its knowledge, and is it permissible to give this money as charity on behalf of the rightful owner, or to give a portion of it to a needy relative?

This bonus is not permissible for you and must be returned to the company as long as it is possible to do so. Donating it is not sufficient unless returning it becomes impossible, in which case it is permissible to donate it to a poor relative.

You must advise the deceptive manager and, if necessary, report him to his superiors, provided that doing so does not cause you significant harm. Your silence regarding his wrongdoing is considered an acceptance of the reprehensible act.