A. We do not know it is a Cylon ship. It could be the Galleon. Remember, Boomer said that the Cylons knew more about the Colonials religion than the Colonials and they were using the sacred texts and other sources the Colonials didn't have. They went to the trouble of telling the story of the exodus from Kobol and naming the ship. The Cylons may have found the Galleon adrift in space. The "resurrection ship" might be a referent to the Galleon. As a result of her mission in the exodus, the human civilization was resurrected on the 12 colonies; she was abandoned and set adrift among the stars. Now, she has been resurrected by the Cylons who are using her.
B. Another possibility: The Colonials are capable of building large stations like Ragnar. It stands to reason the Cylons have a similar capability. This ship could be some sort of command and control hub. In TOS, Gamoray was their outer capital. If they are borrowing at least a few bits from TOS, then this could be the new BSG's equivalent concept. Rather than a large city on a conquered world as in TOS, the Cylons have constructed some sort of large mobile command center the size of say, Ragnar Station. Whereas Ragnar is parked, this one isn't parked.