It's pretty simple. You just add both spouses to the person who is the common parent of the children, and then add the children either from the profile of the common parent (in which case it will give you checkboxes at the bottom of the page to choose the other parent), or from the page of the other parent. You can also note the date each marriage ended, to make it more clear if it isn't a sister-wives type situation ;)
For example, John Smith married Jane Jones and had a son, Sam Jones. Jane died, and John remarried to Sally Brown. They had two children, Jimmy Smith and Katie Smith. On John's profile page, it would show Jane and Sally as his wives, and Jimmy, Katie, and Sam as his children. Each of their profile pages would show their respective mother, and John as their father, and the other children as their siblings.