Yes, kinda. You'll have to reorganize the icons on any new/first time using theme. On the plus side you'll only have to do it once per theme as it saves your settings for each theme.
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Take a couple of screen shot pictures of the way they should be and send them to your computer, then use them to arrange your new theme so as they are all in exactly the same place for you.
As the previous poster says you only have to do it once per theme.
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