RAMPS 1.4 for Stepper Motors

Hi, I just bought a RAMPS 1.4 board for stepper motors. Can somebody tell me if I want to use it without mounting on arduino then what will be the DIR and STP pins. I read their documentation where this code was written:

// For RAMPS 1.4
#define X_STEP_PIN         54
#define X_DIR_PIN          55
#define X_ENABLE_PIN       38
#define X_MIN_PIN           3
#define X_MAX_PIN           2

#define Y_STEP_PIN         60
#define Y_DIR_PIN          61
#define Y_ENABLE_PIN       56
#define Y_MIN_PIN          14
#define Y_MAX_PIN          15

#define Z_STEP_PIN         46
#define Z_DIR_PIN          48
#define Z_ENABLE_PIN       62
#define Z_MIN_PIN          18
#define Z_MAX_PIN          19

#define E_STEP_PIN         26
#define E_DIR_PIN          28
#define E_ENABLE_PIN       24

#define SDPOWER            -1
#define SDSS               53
#define LED_PIN            13

#define FAN_PIN            9

#define PS_ON_PIN          12
#define KILL_PIN           -1

#define HEATER_0_PIN       10
#define HEATER_1_PIN       8
#define TEMP_0_PIN          13   // ANALOG NUMBERING
#define TEMP_1_PIN          14   // ANALOG NUMBERING

In this code, as we can see, that STP and DIR pins for X motor are 54 and 55 respectively. But on Arduino Mega there are 53 pins. So what does it mean? In case you're having difficulty understanding my question, I need to run stepper motors using this module but without actually mounting it on arduino, instead I want to use STP and DIR pins (which I don't know where they are)

Like in this borad:

We can see that if we don't want to mount it on the top of arduino then we can simply apply STP and DIR signals from arduino and it will work. I hope you understand what I mean though I tried my best. Thanks in advance!

Pin 54 is A0

To verify that write a short program with the line

Serial.println(A0);

...R