From my understanding of the episode, here's how it worked:
1) Humans on Kobol make skinjob-style Cylons. My guess here is that the Cylons revolted, which caused the exodus of the 13 tribes (the 13th tribe being the Cylons, who leave for Earth)
2) On Earth, the Cylons figure out how to make themselves as human-like as possible, to the point where they can reproduce.
3) The Cylons on Earth create Centurion-style Cylons, who revolt and, in a simultaneous attack from either side, wipe out everything on the planet, Cylon and Centurion alike.
4) Five Cylons develop (or rediscover) the technology of resurrection, thanks to Tyrol. As the bombs fall, they resurrect to a ship above Earth. They set out for the Colonies to warn them not to create Cylons, as it will end in their destruction ("All this has happened before ... "). Unfortunately, they don't have an FTL drive, so they travel to the Colonies at near-lightspeed. This causes them to travel at a relativistic speed - i.e., time outside the ship lasts 2,000 years(ish), but it only feels like 5 or so to them onboard.
5) They reach the Colonies, only to discover that humanity is already at war with the Cylons. They meet with the Centurions and discover that they are experimenting with creating "skinjobs," their only semi-successful experiment being the first Hybrid. The Five offer to give them resurrection and help them create "skinjobs," if they call off the war. They agree, and the 40-year armistice happens.
6) The Five help create eight humanoid Cylons. The Number Ones (Cavil), however, hate that they have been made so "imperfect," and hate that Ellen has become so attached to Number Seven (Daniel). The Cavils revolt, destroying the genetic material from which the Sevens are made, and destroying the other models (hence, no Number Sevens exist anymore). They wipe the memories of the Final Five, give them false ones, and implant them among the Colonies.
7) The rest of the armistice years are spent with Cavil making changes to the programming of the rest of the Eight (now Seven) Cylons, blocking them from knowing who the Five are. In an attempt to stifle a potential revolt, the Cavils plant inhibitor chips in the Centurions.
8) Adama's mission crosses the armistice line, giving the Cavils an excuse to mount the attack on the Colonies. He does so, manipulating things so that the Five remain alive and can see how awful humans are so that when they finally rejoin the rest of the Cylons, they'll feel remorse for designing them in the way they did.