I am not sure about JR in particular but mixing is done by the master, dual aileron on seperate channels in the receiver is mixed by the master and controlled by a single stick with the slave.
The slave does not control stuff like dual rates, flaps, retracts ect..
Basically the slave (or buddy box) just provides stick inputs (including trim switches) all other functions are done by the master.
That said, I do like the single channel ailerons using a Y harness better.
Again I don't know JR but that is how my Futabas work.