Despite the fact that the Colonies have been warring with the Cylons for over a thousand yahrens, the actual amount of information that they know about the Cylons is very small, and a lot of it is actually probably very inaccurate.
One of the biggest problems that the Colonials face when trying to get information, is how to extract it from a Cylon. Being robotic, they cannot be tortured, and they can simply shut themselves down if it got to that point. And Colonial technology is not up to the task of extracting information from a Cylon's brain through mechanical and electrical means. As such, most of what the Colonials know is guess work.
This page lists some notes that can be given out to players as and when they need it, with gamesmasters decieding how much truth - if any - to give them!
The biggest grey area for anyone non-Cylon, is how they were created. There are currently two main theories circulating around in Colonial think tanks. Not until after the war will one man even begin to suspect the truth.
The first states that the Cylons developed cybernetics and started grafting these onto their bodies, making them stronger, live longer and generally more capable. It is also stated that around this time the Cylon race adopted the human biped form as being more efficient (so, does this mean that the Cylons were aware of the humans long before the reverse was true?). The theory goes on to say that the Cylons become obsessed with cybernetics and it was only with time that they went the whole way and replaced every aspect of their bodies with implants until they became completely robotic, and at that point the living Cylons disappeared and the Cylons we know today came about.
The second theory states that the reptilian Cylons created the robotic Cylons. Why is not clear, maybe their race was dying out and they wanted someway to carry on their work, or maybe they just needed help. In any case the robotic Cylons were created and then for some reason the original Cylons died out. Again, why this happened is not clear. Theorists are pretty certain that the robotic Cylons did not wipe out their creators though. This is the widely adopted theory, and one that most Colonials adhere to. In this view, the robotic Cylons have been around for thousands of yahrens.
For some additional notes on this, see here.
Cylon ship abilities are a known thing, after all, when fighting the same type of ships for many yahrens, you are bound to get to know the capabilities of your enemies. However, getting inside a Cylon ship is a completely different thing, and usually the only way this is done is when a Colonial is captured. As such, information about the insides of Cylon ships is extremely limited and mainly limited to such routes that prisoners take.
A lot of Cylon technology is known by the Colonials - such as details of how their pulsar weapons work - but a lot is also pure speculation - such as how their ships actually fly.
A bit is known about Cylon society, such as the fact that there are several types of Cylon, there is an Imperious Leader, that Cylons have cities and citizens and the like, but actual information on what motives a Cylon is unknown. Most Colonies think that the Cylons just exist to kill or enslave all other life forms, and whilst this is right to a degree, the truth is nowhere as simple as that. However, when you are fighting for your life and very species survival, other motives for fighting are not really deemed that important.