Compiler/EK-TM4C1294XL: EK-TM4C1294XL

I am not sure if I understand your question. A 2 dimensional array is stored in RAM as a single buffer. You can use the EEPROMProgram() function to program that buffer into the EEPROM. Here is a very simple example programming a 2 dimensional array into EEPROM and then reading it back into another 2 dimensional array.

#include <stdint.h>
#include <stdbool.h>
#include "inc/hw_types.h"
#include "inc/hw_memmap.h"
#include "driverlib/sysctl.h"
#include "driverlib/eeprom.h"


//*****************************************************************************
//
// Main 'C' Language entry point.
//
//*****************************************************************************
uint32_t array[4][6];
uint32_t array2[4][6];

int
main(void)
{
    uint32_t ui32SysClock;
    uint32_t i, j;

    //
    // Run from the PLL at 120 MHz.
    //
    ui32SysClock = SysCtlClockFreqSet((SYSCTL_XTAL_25MHZ |
                                       SYSCTL_OSC_MAIN |
                                       SYSCTL_USE_PLL |
                                       SYSCTL_CFG_VCO_480), 120000000);
    // Initialize the EEPROM
    SysCtlPeripheralEnable(SYSCTL_PERIPH_EEPROM0);
    EEPROMInit();

    // initialize the array
    for(i = 0; i < 4; i++)
    {
        for(j = 0; j < 6; j++)
        {
            array[i][j] = i * j;
        }
    }

    // program array into EEPROM starting at first EEPROM address
    EEPROMProgram((uint32_t *)array, 0U, sizeof(array));
    
    // Now read from the EEPROM into the second array
    EEPROMRead((uint32_t *)array2, 0U, sizeof(array2));
}