Thank you for the step by step with JackPilot and SoundFlower. This worked perfectly the first time for me.
l learned the hardway all the things that can go wrong during the set up the first time I took my rmbp away from my desk and came back.
It seems if I want use my rmbp away from the desk with the 2 thunderbolt displays and I pull out both thunderbolt connections it will change the configuration if I don't shutdown both programs first!
When you return to your desk and plug in your Thunderbolt monitors you may (in my case WILL) have redo all configuration settings again. After the first couple of times I became comfortable with it. It now only takes me a minute to reconfigure it all. I did find putting SF, JP and AudioMIDI on my dock makes things easier since this something I have do almost everyday.
This very creative solution that works but, I still hope Apple will write something into the OS that will do this natively.