What is the ruling on a manager exchanging cash for personal money orders, and what should I do about it, and is my salary lawful if I do not report these violations?

The manager's cheating, his taking cash, and his giving money orders is a reprehensible act that must be denounced. There is no need to inform the factory owner if it leads to harm, but participation in it is not permissible. It is not permissible to inform the factory that there are no sales if that is contrary to reality, because it is a lie and deception, and "deceit and trickery are in the Hellfire," and "whoever cheats is not of us." It is not permissible to obey the manager in disobeying Allah. If the manager insists on this, and you cannot ignore his command, then you have no choice but to inform the factory owner, even if it leads to leaving the job.