Didn't Junior make a reference to "the Sopranos finally getting a shot?"
Imprisoned bosses can only be bosses from prison if they have loyalists on the outside. Genovese was able to do it. But after a few years, doing business that way starts to wear thin on the capos. Besides, there's always someone who's trying to unseat a boss whether he is in or out of prison.
Was that from the flashback episode where Junior is upset that Jackie was named acting boss over him?
It is pretty clear that DiMeo had little or no power from his jail cell. We never saw anything in the series to suggest that, although the soldiers never speak badly of him. I suppose as long as he is alive he holds the title though.