As already mentioned, you dont get a single Uplay account. Games bought / activated through steam have a seperate Uplay browser to games bought outside of steam.
I found this as I got the retail (non steam) version of Far Cry 3, I later bought Blood Dragon on Steam. When I launch one of the games, the other game either wouldnt show up at all in my Uplay game library or it would be greyed out and trying to activate the serials in Uplay didnt work.
Launch retail version of Far Cry 3...Blood Dragon steam version greyed out in Uplay.
Launch steam version of Blood Dragon...Far Cry 3 retail version greyed out in Uplay.
Seems totally stupid to me, but hey, thats Ubisoft for you.