You typically add them in the second spot based on their other relationship (the one you are adding now). The most common one is when someone's spouse is already in the tree. One of the options under "add partner/ex" is to partner them with someone who is already on the tree.
Sometimes you end up connecting them to the tree when you find out that their parents are already in the tree, but they are not. Under "Change or delete" choose "Change Parents" then Click on either the Fathe or Mother (or both I guess) and change them to the corect person in the tree.
