How can stolen money be returned to the mother without her knowledge, and is it permissible to deduct the stolen amount from the cost of the courses she requested from the mother?

You must return the money you stole from your mother, or seek her forgiveness for it. The trick you mentioned is not permissible. You can return the money to her using a discreet method that does not expose you to harm, such as sending the money to her anonymously, along with a message explaining that the money belongs to her from someone who transgressed and has repented, in fulfillment of Allah's saying: "And whoever fears Allah - He will make for him a way out."