I have tried this to sort out this very problem/feature on my new site using the inove template for http://www.spartansafety.co.uk (coming soon).
Firstly would not suggest you change Css layout code. Rewriting CSS layouts are no mean feat. If I had the time to this, I would be better of writing this theme all over. anyway i hope this helps with this great theme.
experienced guide:
add an empty text box to stop default widget appearing
Newbie guide below.(me)
login to admin. click on appearance. click on widgets. on right use drop down tag to navigate.
In edit sidebar remove all the widgets that you currently using.
insert text boxes instead with titles only corresponding to each widget direction. e.g. north, south, east or west.
Test in browser. you will now see where each part goes. if you have done it right, you should see a line separating each compas point.
Make a note of the places then plan where you want to put your sidebar widgets.
MY side bar plan
----------------------
North nothing
-------------------------------
west | East
Categories | nothing
-------------------------------
South
Pages
Tags
Now delete the titles of the edit boxes for an empty Places.*
Add the widget to the right widget place and remove the text box.
Test again in browser. everything should be where you need it with no extras.
*horizontal signs may remain so you could jiggle things around like this.
----------------------
North
Categories
-------------------------------
west | East
pages | nothing
-------------------------------
south Tags