There is a wizard in version 7 that will create these underlying rules. There is a lesson and exercise in the SSA course with an example as well.
Your question involves a design question of significant scope that requires a more nuanced answer. Based on your particular example I suggest that you reach out to Pega Consulting for further assistance.
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For this type of requirement configure an File-Listener which reads the file when it is available or placed in that specific folder and read that file after that use Connect-FTP to push the file to destination folder