I am not sure I understand the questions. AFAIK you do not need a condensate in order to form a JJ (I presume you mean a Josephson junction). You do not even need a microsopic model for what is going on in the two banks in ordet to derive the Josephson equations (which is fortunate since this means that we can model high-Tc junctions).
There is a very nice (and simple) derivation of the equations in the Feynman lectures. I like it because it shows that the Josephson effect is very "general" (at least once the equations have been generalized to non-sinusoidal CPRs, Feynman's approach can be easily modified to cover this).
Hence, it is not surprising that it can be created using so many different systems including two BEC.
Alexander Golubov wrote a very nice review of the Josephson effects a few years ago (which includes unconventional current-phase relations); you should be able to find it using Google schoolar (I don't remember the title but I do have it on my computer at work).