I am able to use multipleoutputs feature in hadoop
Yes you can specify that a input format only processes certain files:
FileInputFormat.setInputPaths(job, "/path/to/folder/testfile*");
If you do amend the code, remember the _SUCCESS file should be written to both folders upon successful job completion - while this isn't a requirement, it is a machanism by which someone can determine if the output in that folder is complete, and not 'truncated' because of an error.