To use a region of the internal flash for your own purposes, reserve it in the linker definition. But first, decide which area you'd like to use. Looking at the flash layout,

the sectors at the end are quite large, so you can use those only when you are content with losing a fourth of the available flash (half if you'd like to have a backup sector). In this case, just decrease the amount of flash in the linker config file. If you are using the GNU toolchain, change it from
FLASH (rx) : ORIGIN = 0x08000000, LENGTH = 1024K
to
FLASH (rx) : ORIGIN = 0x08000000, LENGTH = 768K /* last 256k reserved */
or
FLASH (rx) : ORIGIN = 0x08000000, LENGTH = 512K /* last 512 reserved */
update in this case, the last sectors will be left alone by ST-Link, i.e. neither erased (unless you explicitly let it erase all flash) nor programmed.
To use one (or two) of the 32k sectors, we can't just move the beginning up, because the vector table must reside in sector 0, as the reset address is taken from there. we can put some custom structures after the vector table.
.isr_vector :
{
. = ALIGN(4);
KEEP(*(.isr_vector)) /* Startup code */
. = ALIGN(32768);
KEEP(*(.userconfig1))
. = ALIGN(32768);
KEEP(*(.userconfig2))
. = ALIGN(32768);
} >FLASH
and then in the code
__attribute__ ((section(".userconfig1"),used))
volatile const struct cfg userconfig1[32768/sizeof(struct cfg)];
__attribute__ ((section(".userconfig2"),used))
volatile const struct cfg userconfig2[32768/sizeof(struct cfg)];
to be able to get at the values directly from the program.
update in this case, these sectors will be erased and programmed every time you reflash your code. They will be filled with zeroes, or you can put some default values in the arrays in your code.
UPDATE
Unlike most STM32 MCUs, it's possible to move the beginning of the flash on the F7, freeing up the 32k sectors. Adjust both the begin and the length of the flash sector in the linker script, e.g.
FLASH (rx) : ORIGIN = 0x08020000, LENGTH = 896K
to free up the first four 32k blocks, and adjust the Boot address option bytes accordingly, in this case to 0x2008