Okay... we're getting into the "Great Debate" now... :lol
It IS kind of confusing, so bear with me. When the show first began, the distinction was not very clear as to whether it was Sam's body or soul that was leaping. (In fact, the earlier novels written by Ashley McConnell go by the soul-leaping theory, but they don't really count anyway because they're not technically canon.) Once Sam leaped into the pregnant girl in the 3rd season ("8 1/2 Months"), it was pretty much confirmed that it was Sam's body leaping and not his soul. When Sam leaps "into" someone, all he is really doing is switching places with them in time. What everyone else sees is the "aura" of the person that he has leaped into, which is basically just an illusion so that he can assume that person's identity and do what he needs to do. That is why children under the age of 5, animals, and people with mental problems can see beyond the aura, because they exist in some sort of alpha state that allows their brainwaves to perceive the "truth," rather than the illusion.
So, that's why, for example, when Sam leaped into the blind concert pianist in Season 2, he was still able to see with 20/20 vision; or why when he leaped into the paraplegic Vietnam veteran in Season 5, he still had legs. When he stood up from his wheelchair, the orderly saw the "aura" of Ronald Miller floating in mid-air from the knees up. And that's also why when Sam leaped into Billie Jean in Season 3, Al insisted that he couldn't possibly be having symptoms of pregnancy, because Sam was not physically able to deliver a baby. They were afraid that the baby would be born in the future if Billie Jean didn't leap back before she went into labor.
So, in short, when Sam leaped into Will Kinman, it was his physical body that provided the sperm for Sammy Jo Fuller's conception. But since Abigail saw him as Will Kinman, she and Sammy Jo assumed that Will Kinman obviously HAD to be the father (and so did HE).
It's likely that if the series had continued, Sammy Jo would have probably found out the truth eventually, which is probably why MJ and AJ decided to write that when they began The Virtual Seasons. It also seems obvious that she will know the truth when and if the new series gets rolling... otherwise, it wouldn't make much sense for her to be leaping around trying to find Sam.
And don't worry, you're not being annoying. We're always glad to try to explain these types of things (or direct you to a previous post, if it applies). Even if many of the old posts were still here, you'd probably have a hard time knowing exactly where to find the answers to your questions.
Damon