I don't think Paulie was ever an actual underboss. There was no official underboss until Bobby; Tony tried grooming Chris to be one but it didn't work out obviously. Paulie was Tony's number 3 guy but his official rank was capo. He held authority over other capos because Tony decided he could do so. Sil was the second in command so in effect he was both consigliere and underboss. It isn't strictly following the typical family hierarchy but Tony was the boss and he could make the pecking order what he wanted.