How do I managing files with Automator?

Hello!
I looked around in many websites, but didn't found one solution that works for me.
I tried to do one workflow by myself but even so it didn't work.
Maybe this is a simple problem for someone who knows how to work with automotor. But for me it's been a hard task.
I have one "folder A” with files and subfolders, and a "folder B” also files and subfolders (some are the same).
The “folder A”is managed by one software program.
I need when a file is added to "folder A" this will be excluded/deleted from "folder B”.
This will prevent duplicating files.
Someone could help me with this?
Thank you in advance.

How do you attach the pdf to the citation?
Inside the program exist one space to attach the file.
Is it done from within the program (what program BTW?) or is it done from outside the program.
The program is the "Endnote".
Is there some way to tell the program to move the PDF  file rather then copying it?
I suppose not.
If not is there some way to have the program output a list of the PDF files?
I don't know, I suppose not.
Thanks

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