For those trying to implement the solution from this topic, I thought it might be good to give others some additional pointers and tips (as it took me awhile to figure it out):
Continuing the discussion from Multifile upload design:
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There is still an issue if the user hits Cancel on the Upload window: the event “Value Has Changed” for the file uploader will never be hit and the uploader will remain hidden.
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You really need to use a workflow to change the state of the hidden shape that will cover the uploader, using a conditional directly on the shape (as I have) will not work. The covering shape has to be shown and hidden by using Element > Set State in a workflow and a conditional in the shape.
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Make sure to set the “When Clicked” for the Group and NOT the Uploader, otherwise it won’t work (I know thats what it says in the instructions in the other post, but i missed it ;))
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Make sure that before you go back to re-hiding your shape after the upload is complete, that you add a Reset Data for the group containing your uploader and the covering shape, otherwise your shape will be hidden and users will see the ugly completed bar from the uploader again.
EDIT
Ok for those who want a better solution, this post uses the Toolbox Plugin and a very simple Javascript to achieve the goal. I prefer it over the covering with states used before. 
- If the command doesn’t work and you are trying to use a button to open the uploader, try removing the When This Button is Clicked command from the conditionals. Somehow it seems to interfere.