How does an order of protection effect the custody of my children?

Well it depends on the terms of the injunction as to how it would effect the custody of your children. If they injunction is only protecting the other parent, then you still have the ability to make contact and to spend time with your children. The barrier to that could be getting the children because you're not allowed to contact that other parent. So it could be rather difficult and hairy to get the children under certain circumstances. However, if the children as well as or instead of the parent are the ones protected by the injunction, then you are not allowed to have any contact with them in any way.