How do get numbers to display as two digits in C?

You need to use %02d if you want leading zeroes padded to two spaces:

printf ("%02d : %02d : %02d\n", hour, minute, second);

See for example the following complete program:

#include <stdio.h>
int main (void) {
    int hh = 3, mm = 1, ss = 4, dd = 159;
    printf ("Time is %02d:%02d:%02d.%06d\n", hh, mm, ss, dd);
    return 0;
}

which outputs:

Time is 03:01:04.000159

Keep in mind that the %02d means two characters minimum width so it would output 123 as 123. That shouldn’t be a problem if your values are valid hours, minutes and seconds, but it’s worth keeping in mind because many inexperienced coders seem to make the mistake that 2 is somehow the minimum and maximum length.