To remove the blue square, please add this to your custom css...
span#logo-color {
display: none;
}
This is how you create a custom CSS file...
http://www.rockettheme.com/forum/index.php?f=337&t=106162&hilit=tutorial%20custom%20css&rb_v=viewtopic
When we release upgrades template files will change and you will have to reapply all your changes again (that's if you can remember where they all are). If you keep your changes in a separate Custom CSS file you'll have no issues upgrading.
Regards, Mark.
If this resolves your problem then please edit your