I've been holding on to this way too long and I suppose I should share it. I think it's especially appropriate to share it now since, apparently (according to the spoilers), this theory is NOT how the show will evolve. As such, this is less of a theory and more of a "how it could have been".
Note: There are NO spoilers in this entry.
Gaius Baltar & The Everlasting Project
Baltar is, first and foremost, a self-preserving egomaniac and secondly a genius. As such, he is afraid of both death of body and death of legacy. Before the Cylon invasion, I think he was working on a two-faceted uber-project: cheating death while ensuring legacy. To accomplish this, Baltar needed a way to preserve the human consciousness in an eternal form. He realized that an automaton is an excellent form for this.
He worked to devise a means whereby a human's consciousness (i.e. "soul") can be mapped into an electronic (digital) machine. To fund his efforts, he advertised this technology to a select few at extremely HIGH costs. Sharon Valerii, for example, is the only child in her family. Her parents might be easily persuaded, then, to do anything to save her life. If Baltar promised them eternal life for their daughter they might buy it.
The Cylon Factor
The Cylon's seem to truly believe that they are destined to abolish the human race...including the 13th tribe. Baltar needs some Cylon collaboration to overcome some hurdles in the technology. A partnership is formed and the Cylon's see this as an opportunity to infiltrate some of the aspects of human civilization in order to execute their plan of finding (and, presumably, destroying) the 13th tribe. When combined with the fact that Baltar can use his plan to make money, the Cylon's see this as a perfect opportunity to collaborate.
The Original Five
Baltar crossed some bizarre plane of existence when experimenting. The first five models went crazy (whatever that means) as a result of the imperfect mapping process. However, they are not dead. I haven't actually theorized on what/where/when they are. As D'Anna Biers continues her experiments this may become more apparent (and, obviously, more detrimental to my conjectures posed herein). Nevertheless, the original five are not discussed because they are not dead but not whole.
Creating the Models
As part of the plan, Baltar's memory is modified and he is placed in his Cylon body (as appropriate) to execute his role in "The Plan". This procedure is copied for Sharon Valerii, D'Anna Biers, etc. etc. I suspect that one or two of the models are not direct human maps such as Caprica Six. The models do not know their own history specifically but understand the history in general. Furthermore, Baltar is programmed to "discover" that he is a Cylon. Instead of being told, his discovery process will unlock some vital portion of his Cylon brain allowing him to further execute the plan.
The Plan
My conjectures above do not, unfortunately, address "The Plan". However, I have some conjecture on that as well. I think there are possibly two plans in place. The Cylon Plan is / was genocide of the human race. As indicated in the series this plan may have changed but is still a possibility. The Baltar Plan is to find Earth and become a deity of sorts. He is, after all, a genius and Colonial technology exceeds (even if only slightly) the technology of Earth circa 2006. So if Baltar finds Earth at or before Earth Year 2006, he will, most likely, be seen as a god of some kind. Arthur C. Clarke wrote that "Any sufficiently advanced technology is indistinguishable from magic." Perhaps Baltar is hoping to use this concept to his advantage.
Summary
All in all, I do not know the plan (and that is a frustration I have with the series). As such, my conjectures above about the history of the models and back story of the five are potentially irrelevant and probably incorrect. Nevertheless, it has been fun to speculate!
In the interest of readability and time I have kept this entry as short as possible. I welcome your feedback and thoughts and hope to provide additional detail based on your comments.