Concrete5 has a very powerful feature, called scrapbooks, which is very useful for reusing blocks on your concrete5 site. You can follow this link to watch a screencast explaining how to use the scrapbook: http://www.concrete5.org/help/editing/scrapbook_defaults/.
One very useful thing about the scrapbook is that you can automatically add a block from the scrapbook to your theme. If you have concrete5 version 5.3.3 or later, there should be a block included, that is called 'My_Site_Name' in the 'Global Scrapbook.' This is the block that concrete5 uses to display your site name in your themes. If you do not have this block in your Global Scrapbook, you can add just it and it will still work.
To change the logo click on 'edit' next to that item in the scrapbook, and you can edit it just like a normal content block. Anything that you put in this block will show up in the logo section of a theme that makes use of this feature. So you can add any text you want or even an image of your logo, that you want to show up in the logo section.
Thats all there is to changing the logo in our new themes, if you are using version 5.3.3 or later.