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For this you would have to edit the theme.html file located in themes/default directory.
You would do this for any theme that you upload and run on your server, The theme.html file is where you change your logos and other page elements.
To help clarify, Templates control how each block and other elements appear in terms of layout, while the theme takes care of the overall general layout of the site, such as colors, tables, link and text colors etc.
A very common question, so I hope this helps some.
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