I think a lot of people had that biblical parallel (Jacob wrestled the angel and the angel was overcome, Lucifer cast out of heaven, etc.). Honestly, I think I'd be fine if they didn't wrap up the origins of the two specifically. It'd be enough to say that Jacob & Flocke (Fake Locke, which I read somewhere and kind of liked) are two of a kind, not from around here, and related to the island in someway. That would allow for a 'spiritual' kind of interpretation (the island as a cage for the devil) or a sci-fi interpretation (alien prison). If you get too explicit with that answer, you're likely to alienate some or part of the fanbase, because they'll lose interest based on that point rather than the arc of the story as a whole. We need some more info on the two, of course, but I'm fine without the full backstory. Actually, the angels vs. aliens idea (and those aren't the only two possible interpretations, of course), kind of lends itself to the fate vs. free will the show has been toying with the entire time (angels implies a higher power controlling our destinies, aliens implies everything has been happening as a logical result of technologies we don't understand, not because there's a guiding hand).
The structure of the show itself has now gone into the grey area between science and faith with the two parallel timelines. It's kind of an illustration of Schrodinger's cat, the quantum mechanical thought experiment. If you don't know what it is, check out the wikipedia article:
Besides being another variation on the Magic Box idea, it's important to know that from our current theory of science, the cat is both alive and dead. Not one or the other, but both. The only way that this situtation is resolved is with the direct observation of an outside observer (lifting the box and looking at the cat). So who on the show so far is independent of the timeline? Desmond.
And the timelines will converge at some point, as Katie mentioned. Faraday used the analogy of throwing small stones vs. a boulder in the stream as a way to disrupt the flow of time. And boulders will disrupt the flow, granted, but a large enough river or stream (or a small enough boulder) will reconverge after hitting the boulder, although it will flow separately around the incident.
I also think that the island storyline is going to center on resolving mostly mythology points of the show, where the reboot of the 815 story is going to be character-centric. But when the two points catch up to each other (probably in one of the last few episodes of the season), stuff happening in the alternate timeline will matter to the outcome of the show.