What is the ruling on an employee taking commissions, incentives, or cash payments from sales representatives in exchange for purchasing goods, or settling checks early, or stamping invoices that do not belong to his institution, without the employer's knowledge?

You are not permitted to take a commission from customers without the employer's knowledge, as you are his agent and employee. An agent does not act without the permission of his principal, and an employee is entitled to his wage for his work and should not request additional commissions. What you are doing also involves other forbidden acts such as forgery and deception when stamping invoices that were not issued by your establishment.