What is the ruling on taking commission from both the merchant and the customer at the same time, without either of them knowing about the other's commission?

There is no objection to taking a commission from both parties to a contract or from one of them. This is called brokerage (samsarah) and falls under the category of permissible ju'alah (stipulated payment for a service). It is a condition that the party from whom it is taken is aware of it.

If your work is merely an agency for purchasing, then ownership of the commodity is not a condition. However, if it is a sale of a specific commodity, it is not permissible before possessing it, based on the Prophet's (peace be upon him) saying to Hakim ibn Hizam: "Do not sell what you do not possess." But if the commodity is described in a liability (dhimmah) and is not specific, then ownership is not a condition, and the sale falls under the permissible category of salam (advance payment sale) with its conditions.