The way I have my FX8 and JP2C setup, I control the channels and configuration via Scenes in the FX8.
I don't have the documentation near me right now, so you will need to look up the exact numbers you want in the MIDI implementation section of the JP-2C.
The FX8 can send CC#s to the JP-2C, so it is a matter of setting each Scenes to send specific CC#s.
In the JP-2C manual find the CC# for the configuration you would like (Channel, Loop On, Shred ON/OFF, EQ, Reverb, etc.), then have the Scene in the FX send that CC#. In this way, you would not need to touch the JP-2C each time you want to change anything. You just set the CC# on the FX8.
In my main preset, I set the 8 buttons to choose between 4 scenes (bottom row) and toggle 4 FX (top row).
Scene 1 - Channel 1, no EQ, Loop On, No Reverb (the loop should always be on if you are using the 4 Cable Method)
Scene 2 - Channel 2, EQ 1, Loop On, No Reverb, Shred Off
Scene 3 - Channel 2, EQ 1, Loop On, No Reverb, Shred Off (I also use this channel for my lead and have different FX and levels applied in the FX8)
Scene 4 - Channel 3, EQ 2, Loop On, No Reverb, Shred Off (Secondary lead sound)
Not sure if this helps or not, as it is more concept level and not step by step.
~Icarus