Pete is totally correct. Voltage is a differential. And as he pointed out, as long as you don't common "ground" them, you're fine. In my case, I'm hooking up to LEDs which don't have a "ground", per sae, but just a '+' and '-'.
I would never try this concept on anything that does truly ground itself, such as a receiver, or the FC, or any of the other components that connect to eachother. Those all have common ground running through them.
Maverick, to answer your question, I'll connect the '-' of the first bank of LEDs to the Gnd wire of the LiPo, and the '+' to the 3S wire, thus getting the ~12V. Then for the second bank of LEDs I'll connect the '-' to the 3S wire, and the '+' to the 6S wire, thus getting another ~12V. Then effectively I'm leveling the load on both halves of the battery.