Like Guy, my program of choice is Brothers Keeper. I have been using it since the DOS days of 1994/5. It is as easy to use as PAF, if not easier, so well worth having a go with the shareware version.
If you add a child to an unmarried person the program will automatically generate a spouse of (not entered), which can be updated later if required.
For the father of the child which is registered under the name of the de-facto although it could not be his I would add a spouse of Unknown (or something similar). BK has note space which is easy to use for explanations of unusual situations.
In addition Brothers Keeper not only numbers the various spouse but it allows unmarried people to be added as partner.
Cheers
Guy