Sharing the low voltage rail of unknown potentials... How to make Proper Floated Voltages?
But let's make it more complicated by assuming I can't guarantee that the 200 volts across the cap is +200 and 0. It might be +100 and -100 (or even +10 and -190), whereas my battery might be +12 and 0 relatively speaking.


You can pick any node in your circuit you want and declare it to be "ground" for that circuit. So you can pick the more negative terminal of your capacitor and call that ground. Then you know the positive terminal is +200 V (relative to the ground that you defined).


  If I simply connect the 12 volt battery right into the circuit, will its low potential automatically match up (Float?) to the low potential on the high voltage circuit, thus guaranteeing a 12 volt difference to between the Gate and Source of the mosfet?


Yes. If you connect a net of an isolated circuit into your circuit, you then make the potential of the two connected wires equal. In this case, you make the voltage of the negative terminal of the 12 V battery 0 V by definition.


  And for a more advanced system: What if the 12 volts isn't even supplied by a battery? What if it's just another capacitor bank?


What really matters is Kirchoff's Voltage Law. If you add up all the voltages of the branches around a loop, they must add up to zero. The law doesn't care which node is labelled as ground.


  And for a really complicated system: ...


Without a schematic of what you connected, nobody can tell you why that situation caused a problem.