If memory serves me correctly, Jackie Aprile was only acting boss while Eckley DiMeo was "a guest of the government." That's a plot hole that was never resolved. DiMeo is mentioned early on in the series, but then just vanishes.

The only plausible thing I can think of was that Jackie was a stronger earner -- he had the plumbing business, plus what he looted from the union pensions. The Feech card game heist helped his reputation as well.

Junior probably respected and deferred to DiMeo's wishes, but this was never really fleshed out in Season 1.