I was STILL looking for a solution to this problem this morning. I am using Endnote 7 on a Mac. While it still doesnt seem to be a function of Endnote, there is an easy workaround.
As above, the problem is that when you Import PDFs (using the Auto Import feature personally) they will automatically save to the default library (in sub-folders labelled with numbers - for whatever reason). Transfer these to your desired destination folder by:
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Creating a blank file on your desktop, or wherever.
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Highlight (Cmd+A) all the PDFs subfolders (with numbers) from the past week or whatever period of time.
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Copy and paste these to the untitled folder on your desktop.
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in the search bar of the blank folder, type ‘.pdf’ - this will bring up all the pdfs in that folder, out of the subfolders.
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Highlight these (Cmd + A), and copy and paste into your desired destination folder (e.g. called ‘Articles’)
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Delete the blank desktop folder.
Yes, its not perfect as you will have to repeat this process every so often, but I’ve searched for the past hour and this is the only way I can find to manage my PDFs in one accessible folder using Endnote.