ligambi referenced him on that wiretap in asymbolic kind of way. everyone knows who has the power but he just says that to take heat off himself. to put it in lehmann's terms its like the way tony soprano keeps references jr as the boss of this family to every1 when every1 knows this is bs.
I'm not sure what you're saying exactly but, since those tapes came out, the feds now have enough reason to believe Merlino was the official boss all along and Ligambi was acting boss. So, in answer to the original question that started this thread, yes, Merlino appears to have the final say. But Ligambi obviously had a lot of authority; including to hold off making guys Merlino wanted until Merlino got out of prison and could make them himself.
