Here's your problem. ">>" only redirects stdout to the file. Your error message is being sent to stderr.
So, what you want is,
This will take the console output (non errors), stick that onto the error messages, and finally, stick this into your output file (note, out.txt, err.txt are temprory files, overwritten every time).
rcp file_to_be_copied file_to_copy_to 1>out.txt 2>err.txt
cat out.txt >> err.txt
cat err.txt >> output.txt
Implement this in your program however you want (i'd recommend "system();" calls personally).
Or, if your doing a standard "sh" script, just stick it in your script.
Enjoy your day.