There are some corrections that need to be made for better comprehension, but overall your meaning is clear.
Every Sunday we go to church. I haven't had my son baptized yet, because I am waiting for my sister to come with us to the ceremony. I want her to be a godmother for my son.
Every Sunday when we go to church my son sleeps during the service in my hands. Like my daughter, he refuses to sleep in his cot or in a stroller when we go out somewhere.
I hope that this helps :)