Which pins to connect rows/column wires are your choice. When you're working with QMK (or another) firmware, there's a file where you specify what pins you've used, the size of your keyboard matrix, etc. Here's a random config.h file I grabbed out of my QMK source code folder. Here you can see where the matrix is dimensioned and the pins are defined.
As you read this keep in mind that you won't be starting from scratch. You'll look through the QMK source to find a keyboard of a similar size/layout as yours, modify a couple of files, and build the firmware for your board.
/*
Copyright 2012 Jun Wako <wakojun@gmail.com>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef CONFIG_H
#define CONFIG_H
#include "config_common.h"
/* USB Device descriptor parameter */
#define VENDOR_ID 0xFEED
#define PRODUCT_ID 0x6060
#define DEVICE_VER 0x0003
#define MANUFACTURER PHANTOM
#define PRODUCT PHANTOM RGB MOD
#define DESCRIPTION QMK keyboard firmware for PHANTOM TKL
/* key matrix size */
#define MATRIX_ROWS 6
#define MATRIX_COLS 17
// ROWS: Top to bottom, COLS: Left to right
/* Row pin configuration
*/
#define MATRIX_ROW_PINS { B5, B4, B3, B2, B1, B0 }
/* Column pin configuration
*/
#define MATRIX_COL_PINS { D5, C7, C6, D4, D0, E6, F0, F1, F4, F5, F6, F7, D7, D6, D1, D2, D3 }
#define UNUSED_PINS
/* COL2ROW or ROW2COL */
#define DIODE_DIRECTION ROW2COL
/* define if matrix has ghost */
//#define MATRIX_HAS_GHOST
/* Set 0 if debouncing isn't needed */
#define DEBOUNCING_DELAY 5
/* Mechanical locking support. Use KC_LCAP, KC_LNUM or KC_LSCR instead in keymap */
#define LOCKING_SUPPORT_ENABLE
/* Locking resynchronize hack */
#define LOCKING_RESYNC_ENABLE
/* key combination for command */
#define IS_COMMAND() ( \
keyboard_report->mods == (MOD_BIT(KC_LSHIFT) | MOD_BIT(KC_RSHIFT)) \
)
/* Underlight configuration
*/
#define RGB_DI_PIN E2
#define RGBLIGHT_TIMER
#define RGBLED_NUM 20 // Number of LEDs
#define RGBLIGHT_HUE_STEP 10
#define RGBLIGHT_SAT_STEP 17
#define RGBLIGHT_VAL_STEP 17
/*
* Feature disable options
* These options are also useful to firmware size reduction.
*/
/* disable debug print */
//#define NO_DEBUG
/* disable print */
//#define NO_PRINT
/* disable action features */
//#define NO_ACTION_LAYER
//#define NO_ACTION_TAPPING
//#define NO_ACTION_ONESHOT
//#define NO_ACTION_MACRO
//#define NO_ACTION_FUNCTION
#endif