Most of the time, recording a person's birth parents is very straightforward. When you add a person's mother and father, Family Historian will assume by default that these are the birth parents. However, occasionally things can get more complicated.
In Family Historian, as in most genealogy programs, family relationships are stored in Family records. Each Family record allows you to record up to two parents (who can be same sex parents), and as many children as you like. Within each Family record, each child can have a recorded relationship to their parents in that Family record. If nothing is recorded about the child's relationship to their parent, this is treated as implying that they have the default relationship to both parents - namely that they are the birth child of both parents. You can if you wish record that the child was adopted, step, fostered or de facto (accepted as a birth child, even though they may not have been really). You can also explicitly record that their relationship is birth if you really want to - but you are recommended to only do this if you have some particular reason to do so (e.g. if you want to emphasize that the child was the birth child, perhaps because questions had been raised about this). The child can have the same relationship to both parents, or different relationships to each parent. A child could be the birth-child of the mother, for example, and the step-child of the father.
Each child can be listed as a child in more than one Family record. In fact, they can be a child in as many Family records as you like. However, this can potentially create inconsistencies. Suppose a given person X is listed as a child in two Family records. Let us imagine that X's parents in the first Family record are given as Allison and Brian. And X's parents in the second Family record are given as Camilla and David. If in each Family record, Allison and Camilla are each recorded as X's birth mother - that would be an inconsistency. They can't both be. Equally, if both Brian and David were recorded as X's birth father - that also would be inconsistent.
Theoretically, it might seem that there would be nothing inconsistent or wrong in recording Allison as X's birth-mother and Brian as X's step-father in the first Family record, while also recording Camilla as X's step-mother and David as X's birth-father in the second Family record. And it's true that as far as that goes, there's nothing obviously wrong about that. But it is problematic because of the way Family Historian determines who a person's birth parents are (see next).
See also How to Flag a Child as Adopted, Illegitimate, Etc.
When trying to determine for any given person X, who X's birth parents are, Family Historian will look for X's birth Family record. X's birth Family record is the first Family record for X in which both parents are listed (explicitly or implicitly) as birth parents - if there is one. If no such Family record exists, the birth Family record is the first Family record for X in which at least one parent is listed (explicitly or implicitly) as birth parent. If no such Family record exists, X does not have a birth Family record.
Just to be clear, if X has a birth Family record, that doesn't mean that Family Historian will treat the parents in this Family record as X's birth parents. It just means that when trying to determine who X's parents were, Family Historian will only look at this Family record. So, for example, if the father in X's birth Family record is recorded as his step-father, Family Historian will treat X as having no recorded birth-father.
What this means is that in the situation mentioned earlier, if you want to have a Family record in which Allison and Brian are recorded respectively as X's birth-mother & step-father, and if you want to have another Family record in which Camilla and David are recorded respectively as X's step-mother and birth-father, then for Family Historian to be able to correctly determine who X's birth parents are (which it needs to do, to calculate DNA information correctly and for other purposes), you need to have a third Family record in which Allison and David are recorded as X's birth-mother and birth-father. All of these Family records can be in any order - most people would probably record them in order of importance from X's point-of-view - but they must exist.
Suppose two people, X and Y, got married twice (having presumably divorced once). Should you record this using one Family record or two? You could record it using two Family records, but our recommendation would be that you should use only one, and simply record both marriage events and the divorce event, within this Family record. If you really want to record it using two Family records, you could. However, if you do that, you should be careful to ensure that exactly the same list of birth children are recorded in each Family record. If you do not do so, this would be another way of recording inconsistent information, which could lead to errors in DNA calculations, etc.