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.