Isolating Mac files from Windows but still being able to copy/paste?

Hi,
I have just started using PD. I notice that at the moment all my files on my Mac are also in my PD Windows. Is it possible to isolate the two OS files? But I still want to be able to copy/paste/drag the files between the two, I just don't want every file to be present in both of them at the beginning. Whenever I need a file to be on Windows, I should be able to copy/paste it from my Mac.
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