The easiest way would be to remove the part of the string just after what you want to delete and then make the change. After you make the change, concatenate the part you removed earlier.
Code:
#include <iostream.h>
#include <string.h>
int main ( )
{
char *newVal = "12345";
char string[1024] = "file,tcp,ftp,SF,5,6,3,normal";
char holder[256];
char *first_cut, *cut_end;
// Hack it up
first_cut = strchr (string, ',');
cut_end = strchr (first_cut, ',');
strcpy (holder, cut_end);
strcpy (++first_cut, newVal);
strcat (first_cut, holder);
cout<<string<<endl;
return 0;
}