As much as we all want to think that things are so structured in the family, the reality is that these guys dont carry around badges saying "underboss" or "consigliere". Tony took over the family in the middle of the first season. He maintained that status till the last episode. He was not considered to be the official boss until the 5th season. Recall the episode where Janis gets pinched for assaulting a soccer mom. In that fictional tv report, the reporter refers to Janice as the sister of "reputed New Jersey mob boss Tony Soprano".
As far as the Underboss situation, there was no technical underboss after Tony took over until Bobby got the position in the last season. Silvio was the number 2 in the family, whether you wanna call him Counselor or Underboss or whatever, he was number 2. Paulie was a Captain throughout the whole series. The only time there was an underboss was when Bobby got it in the last season. There was a point in the 4th season, when it may be argued that Chris had stepped into the underboss role, however, after his heroin problem was revealed he lost that opportunity.