For the whole season we thought of ZOOM's Earth as Earth 2, and Jay at the end says to call his world Earth 3, then there is Supergirl that for now we could say is Earth Supergirl or Earth S.
However in the finale ZOOM states that Team Flash's Earth is the central Earth from which all other alternates have emerged.
Thus we should consider Team Flash's Earth to be called either Earth Zero or Earth Prime, this would make ZOOM's Earth to be Earth 1 as it is the first parallel world for them to have encountered, and thus making Jay's to be Earth 2 which makes things a bit more sensible since in the comics Jay and the JSA are all from Earth 2.
Supergirl's Earth would still be Earth S for now, pending any upcoming merges.
Yeah they messed up the numbers on the show, might be too late to fix it though. They called Zoom's Earth, Earth 2 for the last year.