I'm think that the whole "one larger story" and "each standing on its own" contradictions will be resolved this way: the whole 16-issue arc (assuming 4 issues each) will broadly deal with what happens on LV-223 as a result of the meddling by the crew of the Prometheus, but each one will be set at different points in the series chronology. As much as I hate to be a downer, when DH says things like "characters from one series will cross over to others!" I remember that with both TWW and Xenogenesis, that basically amounted to passing references, short flashbacks, or characters drudging up old video recordings. We'll have to wait and see, though.