you'll need to upload to a separate folder, when the import script is run it'll ask you for the location of the files, then it'll import them into the downloads folder you specified in the Downloads II options.
Depending on the size of the files you may want to do them in batches. Like I have DJ mixes for download...most of them about 80-100+MB, so I had to do them in batches of about 15 to prevent anything from stalling out.
Hope that helps.
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