My fear is that I will be rejected on all counts now...and that we won't even be allowed to marry or be together or something, all because I didn't know that my visitors visa isn't good six months back to back, only six months out of the year or once in a while or whatever.
It's good to remember that the 6 months out of 12 is a
constructive rule rather than law. There's lots of American visitors who are in and out constantly and whose time in the UK adds up to more than 6 months. However, those visitors generally have a reason to be here, which is usually business related.
A two year run for a trial relationship is likely to likely to raise eyebrows, but I don't see anything that rules it out. But you can take it on board that it's cases like this that get their backs up and ultimately make it more difficult for all Americans to have trial relationships here.
Regardless of which route you go: UP, fiance, or spouse, I would offer the idea that your application have a very strong financial and accomodation case from your bf. Why? Because, if it's a weak financial case from your bf, they will (quite rightly) think that you were working during your time here. And that's a show-stopper.
The other thing that comes to mind is if they decide to delve into it, it might pay to think up a convincing reason why you were in the UK for that length of time. The notion of waiting for friend's babies to be born is weak, especially over the course of 2 years. As for having lots of international guests, even the royal family weddings don't take that long to arrange.
Finally, to your question about refusals: if you are refused you can appeal, but if you apply again while the appeal is in progress, they consider that you have abandonned your appeal. And for your other question about applying at the same time: you can apply for anything you want as often as you want, BUT they have to be made 1 at a time. Hope that helps!