Vera,
No worries, if you have the store window turned off, it won't get added.
Customization of the store window, changing colors and such, should work without a problem. Have you talked with our support staff about this? Do you receive error messages when you try to update the settings?
To quickly run down how to change colors...
Goto the "Store" tab.
Click the "Store Window" link on the left.
Click the "Edit Store Window" link.
On this page, you should then be able to select a different color theme and then hit the "Update Preview" button to see how it looks. When you've found one you like, you can hit the "Save Changes" button.
Hope that helps.
-Kevin