I'd imagine the easiest way to trace one's ancestry to Charlemagne would be to trace one's ancestry to a known decedent (which would still involve what Kindler's family, and my great-uncle did (he also used tomb stones)). I'd also imagine that a lot of that would result in Molly stopping at some other king, though I don't know enough about any dynasty to say whether or not a lot of kings descended from Charlemagne. I would imagine that it would be pretty rare to be descended from an ancient king's line that didn't have any other kings in it, but, once again, such things are way beyond my competency.
Molly's research could have been digging through family documents or records that someone else had already gathered.