What should I do for the slaughter to be acceptable, and is my slaughter valid, knowing that the owner of the slaughterhouse took the hide and entrails in exchange for the slaughtering fee, and I did not know that it is not permissible for him to take anything from them as payment, and we did not agree on a fee?

The rules of Udhiyah (sacrificial offering) apply to the Aqiqah (sacrifice for a newborn). It is not permissible to give the butcher any part of it as wages. What you did was an error, and you are required to give in charity the value of what the butcher took from the hide and entrails. Your Aqiqah is valid and is not invalidated by what you did.