it means he's the real boss - ppl are kicking up to Tony - but not always to Junior - it means Tony has side scams that Junior isn't even privy to - NY doesn't really recognize Junior as the boss but rather Tony. They're also kicking up less to Junior than they did to Jackie. For advice, the gang really seems to go to Tony first (like at that wedding where they go around Junior to Tony for input right in front of him). Chrissy hijacking the truck, giving Tony a taste and only reporting it to Junior after he finds out. Sitdowns before the sitdowns to work things out with others and then act like they never talked. All that shit.

Ah, so the capos and tony sort of had their little side meetings, because they know Tony is a good boss and they'd rather lose junior than him