Is it permissible for me to set a profit margin for my private company or a commission for a sale operation, knowing that I have informed my employer about the commission for the intermediary, and I preferred that the client receive the items from the company I work for?

If you are going to buy the goods from your company and then sell them to the broker, there is no harm in setting a profit margin, because it is a permissible sale as long as it does not involve exploitation, fraud, or deception. However, if you are going to act as an intermediary between your company and the purchasing broker for the client, there is no harm in agreeing with one or both parties on a commission for your effort, which is known as brokerage.