[mgatten]

Some files are shared by all skins. The company logo is one of them.

In the admin area, under the Content tab, click Edit Templates.

Click "Common Files" to enter that directory, then click the images directory.

At the bottom of that screen you can upload files to add to the directory or replace existing ones.

To replace, be sure the filename is exactly the same. To avoid breaking layouts you should also try to make the replacement image the same size as what it's replacing.