In the series the Underboss position seems to be unclear. In one episode Tony says Sil and Paulie are getting a bump(Sil to consigliere and Paulie to capo or underboss) but later on it seems like he promotes Bobby to underboss. Any thoughts?

You got it right. In season 1 Junior's underboss is Joseph Sasso (you only see him for a second). And then once Tony is in complete control Paulie would be underboss, and then in my opinion it would be Christopher for a short period of time, and then near the end of the series Bobby.

The underboss position is redundant in the DiMeo/Soprano family as Tony usually takes care of most of the stuff. Unofficially, I guess Paulie is the underboss and then in Season 4 (when Paulie's in jail) Christopher gets bumped to capo of Paulie's crew (and unofficial underboss)
Later on the title goes to Bobby Bacala.

Thanks. I agree that Tony seems to act as his own Underboss at times. Paulie seems like more of a capo to run Tony's old crew, and Christopher eventually takes that crew over too. If anyone seems like an underboss it would be Bobby in season 6 to me.

Another thing I noticed is that after Johnny Sack takes over, he's got no official underboss. We know that Jimmy Petrille (the rat) is his consigliere but the underborss title is never mentioned... which is weird since Johnny was Carmine's underboss. I guess Phil served as the unofficial one, and later street boss after Johnny gets snatched by the feds.

Although Tony was egotistical, impulsive and selfish, he was the master manipulator. He relied on titles to keep his men in line.