My solution to CS50x Problem Set 2 - Substitution. Feel free to critique or ask questions.

substitution.c

#include <stdio.h>
#include <cs50.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>

int main(int argc, string argv[])
{
    //checks if user has inputed a command line argument, if not returns error message
    if (argc == 2)
    {
        //checks if command line argument is 25 characters long, if not returns error message
        if (strlen(argv[1]) == 26)
        {
            int count = 0;
            for (int i = 0, n = strlen(argv[1]); i < n; i++)
            {
                //checks if each character in command line argument is a letter, if not returns error message
                if (isalpha(argv[1][i]) == 0)
                {
                    printf("Usage: key must only contain alphabetical characters\n");
                    return 1;
                }

                for (int p = 0; argv[1][p] != '\0'; p++)
                {
                    //counts each character and each repitition of character and stores it in variable "count"
                    if (argv[1][p] == argv[1][i])
                    {
                        count++;
                    }
                }
            }
            //if count is larger than 26 due to a repitition, returns error message
            if (count != 26)
            {
                printf("Usage: key must not contain repeating characters\n");
                return 1;
            }
        }
        else
        {
            printf("Usage: key must be 26 characters long\n");
            return 1;
        }
    }
    else
    {
        printf("Usage: ./substitution key\n");
        return 1;
    }

    //gets the text the user wants to encode and stores it in variable "plaintext"
    string plaintext = get_string("plaintext: ");

    //stores command line argument (user's intended key) in variable "key" for neater code later on
    string key = argv[1];

    for (int i = 0, n = strlen(plaintext); i < n; i++)
    {
        //makes sure only letters are encoded
        if (isalpha(plaintext[i]) != 0)
        {
            //separate algorithm for uppercase letters in the user's text-to-be-encoded
            if (isupper(plaintext[i]))
            {
                //establishes variable "key_place" for matching the appropriate letter to the key's equivalent
                int key_place = (plaintext[i] - 65);

                //if the letter in the key that is supposed to replace the original letter is of different case, switches the case in key
                if (islower(key[key_place]) != 0)
                {
                    key[key_place] -= 32;
                }

                //substitutes the original letter with the corresponding letter in key (which has now been case-matched)
                plaintext[i] = key[key_place];
            }
            //separate algorithm for lowercase letters in the user's text-to-be-encoded
            else if (islower(plaintext[i]) != 0)
            {
                //establishes variable "key_place" for matching the appropriate letter to the key's equivalent
                int key_place = (plaintext[i] - 97);

                //if the letter in the key that is supposed to replace the original letter is of different case, switches the case in key
                if (isupper(key[key_place]) != 0)
                {
                    key[key_place] += 32;
                }

                //substitutes the original letter with the corresponding letter in key (which has now been case-matched)
                plaintext[i] = key[key_place];
            }
        }
    }

    //prints out the encoded text and ends program
    printf("ciphertext: %s\n", plaintext);
    return 0;
}

Thank you for posting this!! I have a hard time getting started or should I say knowing where to start! You gave clear and precise comments stating the purpose, so now I can go through the order of steps creating mine!