You enter the information as you have it. What is important is that you have the relationships between the Natural Mother and Father with the Child. Don't worry, yet, about what that relationship is.
You can adjust those relationship Settings on the Relationship button, on the People Workspace, Person Tab. There is where you define the relationships.
But you want to look at the relationships between the mother and father (not defined by marriage) and the relationship between the parents and the children.
What version of Family Tree Maker are you using? Help, about.