In order to sort the words, I recommend that you create an array of char *, in which every element of the array points to a word.
In order to find the start of the words and to make the words properly terminated by a null character, I recommend that you use the function strtok or strtok_r.
Here is an example:
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define MAX_WORDS 100
//custom compare function for the function "qsort" which does
//nothing else than call the function "strcmp" for comparison
//purposes
int my_compare( const void *a, const void *b )
{
    return strcmp( *(const char**)a, *(const char**)b );
}
int main( void )
{
    char *words[MAX_WORDS];
    int num_words = 0;
    char *line = NULL, *p;
    size_t len = 0;
    ssize_t lineSize = 0;
    //prompt user for input
    printf( "Please enter words to sort:\n" );
    //read one line of input
    lineSize = getline( &line, &len, stdin );
    if ( lineSize <= 0 )
    {
        fprintf( stderr, "Input error!\n" );
        exit( EXIT_FAILURE );
    }
    //remove newline character, if it exists
    line[strcspn(line,"\n")] = '\0';
    //find first word
    p = strtok( line, " " );
    //loop until no more words are found, processing one word
    //per loop iteration
    while ( p != NULL )
    {
        //verify that we are not overflowing the array
        if ( num_words == MAX_WORDS )
        {
            fprintf( stderr, "Too many words for array!\n" );
            exit( EXIT_FAILURE );
        }
        //add pointer to found word to the "words" array
        words[num_words++] = p;
        //find next word for next loop iteration
        p = strtok( NULL, " " );
    }
    //now we can sort the array
    qsort( words, num_words, sizeof *words, my_compare );
    //print the sorted words
    for ( int i = 0; i < num_words; i++ )
    {
        printf( "%s\n", words[i] );
    }
    //cleanup
    free( line );
}
For the input
apple orange banana dog cat
this program has the following output:
apple
banana
cat
dog
orange
As you can see, the words were properly sorted.