Tried connecting 2 things two 1 battery, smoke ensured
I have friends who have tried to hook up similar things in "parallel" and all they ended up doing was providing a short between the batteries and thus the smoke and very hot wires.  

Take a closer look at your parallel connections (or provide us a diagram) to make sure that you are not just providing a "+" to "-" of the same battery.  It sounds like an obvious thing not to do, but when adding all of the RC connections in you might not notice what is happening.  As a result you are exposing your components to a very large amount of current.

Just a thought, could be something else entirely.  Good Luck