Which flash sector to write into?
You can use any flash sector (or smallest erasable unit).
The first one is required to boot when BOOT_ADD isn't changed for a different entry point.

You will have to specify in your linker that you are using a region of memory for other purposes, or link the configuration to this region already.

See Table 3. STM32F756xx and STM32F74xxx Flash memory organization in the reference manual.  

Please also note Table 48. Flash memory programming in the Datasheet. There are significant sector erase times.

You may also want to investigate eeprom emulation to support more write cycles, or faster writing. But the low sector count might make this wasteful to implement. In that case you might want to get external FRAM/EEPROM.