I'm going to tell my mother I want my step mom to sit with my father during the ceremony
That feels inappropriate. Why would you need to arrange their seats like that?
I'm tired of her. I want her to sit somewhere else during the ceremony
It can be difficult to get seating arrangements right when it comes to mixed families and important ceremonies. However it isn't really appropriate for you to dictate who should sit where without first taking into the consideration of everyone involved. You should talk with your parents, both biological and step, about your feelings and try to find a compromise that will work out for everyone at the ceremony.
I'm going to make a big deal about it, since I'm in control of the wedding.
You can try and suggest a sitting arrangement but I do not think it is appropriate for you to force people to sit with someone they may not be comfortable with sitting next to. I suggest that you talk with you mother as there may seem to be an underlying conflict between you to that I recommend you fix before the wedding.