How to copy stdin into two files?
You need tee.
$ echo 'foo' | tee f1.txt f2.txt or
$ echo 'foo' | tee f1.txt > f2.txtto suppress the additional output to stdout.
I'm guessing your real problem could be how to read from input inside a script. In this case, refer to this question. That will give you something like
while read input; do echo $input | tee -a f1.txt > f2.txtdone