What is the ruling on taking the difference between the amount of money given to me by the owner to purchase merchandise and the actual price at which I bought the merchandise? And if I am obligated to return the money, how can that be done without the knowledge of the owner or his partner?

What you did is a lie and an unlawful appropriation of people's money. You must repent to Allah and return the difference to its owner. You are not required to inform him of the truth of the matter; rather, it suffices to return it by any means. However, if the amount is from the company's funds, then you must inform the person or his partner.