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The theme.html controls the placement, the style.css controls the colors, widths, etc. within the blocks that the theme.html lays out.
You can find more information on the XOOPS wiki for theme editing. You also have to change the settings in system, preferences, general to "update the theme.html" file. (And then change it back when you are done to not update as that will slow down performance if you leave it on).
HTH.