It's interesting - it's sort of vaguely implied that Sue is either Doom's wife or his consort simply from the fact she's his close confidante, but I don't think there's anything to explicitly confirm their relationship, and it's not clear if he's adopted her kids or just rewritten things to make them 'biologically' his. Presumably they were their canon ages (3-4 for Valeria and any random number between 7 and 12 for Franklin) when he called the world into existence eight years ago, so they were never actually 'born' in this world, just existed from the start. Sue doesn't remember Reed, so maybe she and the kids think Doom is their actual father, or maybe they're just aware that he's God and made them exist with no bio-father needed and therefore is technically 'Dad' regardless.