paulie was underboss after tony officially took over the family
after christopher took over his crew he made a comment about "how this was the second time paulie flaunted his authority to his face".......that was in the episode right before chris died in the car accident
tony told bobby to tell junior that he gets to keep his stripes in season 2. which means that junior was the boss (whether he had control or not) and tony was the streetboss
There was never any indication that Paulie was underboss throughout the entire series. Even at the end, the talk was about him taking over the Aprile crew, i.e. a captain. I've posted the stuff below before that shows he was a captain but not underboss.
Season 3: Episode 11 – “Pine Barrens”While they are lost in the woods, Paulie complains to Chris about Tony’s dealings with the Russians. Chris says that it is none of their business. Paulie replies “Fuck that, I’m a captain.” Later on, when Paulie threatens to pull rank on Chris for peeing outside the van window, Chris says “Fuck you Paulie, captain or no captain, right now we’re just two assholes lost in the woods.”
Season 4: Episode 2 – “No Show”At a meeting involving Silvio, Ralph, Bobby, Chris, Patsy, and Little Paulie, the discussion comes up about no-show jobs on the Esplanade construction site. The decision is made to give a no-show job to Paulie, who is in jail, as well as a no-show job to Chris, who is made acting captain over Paulie’s crew.
Season 5: Episode 1 – “Two Tony’s”Chris goes out to dinner with Tony, Silvio, Feech, and Paulie. Beforehand, Chris had to borrow money from Adriana because he was "low man" that night and so was expected to pay. At the end of the meal, Chris and Paulie fued over who ultimately has to pay. If Paulie was underboss, he would have been outranked by Tony alone, and would not have been bickering with Chris over who picked up the check.
Season 6: Episode 20 – “The Blue Comet”Phil decides to go to war with New Jersey and makes his decision known to Butch and Albie. “We decapitate and do business with whatever’s left” he says. Later, Butch holds a meeting with other family members about who exactly to hit. They decide to hit who they identify as the top three guys – Tony, Silvio, and Bobby. One of them expresses his amazement that Bobby has risen so high after being “Junior’s driver.”
Upon being warned by the FBI that New York is planning to strike, Tony gives the order to hit Phil to Silvio and Bobby. They, in turn, pass along the order to Paulie, who who clearly resents taking orders from Bobby. Continuing on down the chain of command, Paulie gives the order to Patsy, who arranges the hit with Corky, the go-between with the Italian hitmen.
In the latter part of the episode both Silvio and Bobby are shot by New York hitmen, though Tony manages to evade them. Paulie is never a target, as he likely would have had he been the underboss.
