I've got a fresh install of D7.9 and have enabled the 'Seven' theme which has an option to override the default logo in Appearance -> Settings. I have uploaded a logo file and can see it via ftp but it does not show up on the site. Have I missed a step or does this theme not support logos out of the box?
The logo for the theme selected is added to a php serialized array in the system table under the info column. It is advisable to not use FTP to upload the image but instead of the Admin UI under the themes section to do so.
Click Appearence > Seven 7.8 > Settings
Then scroll to "Logo image settings" and uncheck "Use the default logo".
Click "Choose File" and pick the logo image file.
Click "Save configuration" and your logo should show up in the site. If caching is enabled, the caches might have to be cleared.
Edit: The page.tpl.php file for the seven theme does not have a section to display the logo. Not sure if this is a bug or just a design decision. Either way, there is no way to show a logo in the seven theme at this time.