In the first part of Season 1 we heard about how DiMeo was Boss in prison for life and Jackie Aprile was his 'Acting Boss' but when Junior stepped up after Jackie's death he was cited as 'The Boss' and afterwards DiMeo wasn't mentioned here's my theory as to what happened.

-When DiMeo goes away Jackie is named Acting Boss also holding the position of Underboss like Tony when he was 'Acting Boss' for Junior.

-Jackie gets cancer and Tony begins to take up responsibility for him after Jackie's death he proposes Junior to take over

-Junior was the last person to owe DiMeo any real favors at that point and was considered the official Boss indefinitely, DiMeo couldn't really do much by that point and even if he could what's the point he's in jail for life.