I am so, so sorry. I realized now that all the confusion stemmed from the fact that Lucifer rising was at the end of season 5 and Crowley's deal with Bobby didn't actually happen til middle of season 6 and the boys did not come looking for the bones until then.
That in mind, i have to write a "look into the past" told by Sammy hanging upside down from Harry's ceiling on why they're hunting Crowley. That might take a day or two so please be patient.