Go back to your template package. The folders you need to upload to your server where you uploaded the Magento files are

a) “app” and “skin” folders located in the “theme###” directory of your template package;

b) “media” located in the “sources” directory.

When you start uploading these files, it is going to ask you if you are ready to replace them, since Magento already has files with such names. Confirm the replacement.