For packages already in your download list or in linkgrabber, yes, you will have to change it. Though you can do that by highlighting everything then right click and select Properties. That'll change everything if you clear the checkbox.
For getting that to happen automatically, I have to ask,
How are you adding files?
When you add files manually in the linkgrabber tab, it should ask where you want the file saved. If it says something like C:\Downloads\<jd:packagename> you need to remove that last part and click save. Any subsequent files you add will pick up that change.
With the clipboard monitor, U think if you do the above it will work, but I haven't been able to prove it since mine doesn't set subfolders by default.
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