So, I have a theory...
What if, way back in the mists of the mini-series, Baltar died when the nuclear blast hit his home?
What if, when he died, he was resurrected using the same technology that resurrected Starbuck? I would imagine the Cylons would be able to clone from the pile of radioactive ash that he should have been
What if, during the resurrection, the Cylons implanted Head-Six? Or, failing that, Head-Six manifests because his DNA was irrevocably mixed with Caprica Six during the explosion. (I know DNA doesn't work like that, but when has that ever stopped sci-fi writers from butchering science for a good story?)
I think that would explain a fair chunk of what's gone on in the series, not least how he was able to survive that explosion.
And, by the way, I've not seen episode 19, so if this is affirmed or denied in the episode, I'll disavow ever writing it :)