You can set your cover up in different ways so it makes sense that you can upload different versions of your logo to suit the background you've set up.
Changing the logo
Click Templates > Cover Templates > Edit.
From there you just click on your default logo and you can browse to upload a different version. Generally speaking it's better to use a version of your logo with white text and a transparent background.
This is how you want it to look
Not like this...
Removing your logo
Sometimes you might want to remove the logo from the cover and do something creative with the background image. You can't completely remove the logo but you can make it invisible.
All you need to do is download this image and simply replace your existing logo with this transparent graphic and it'll vanish.
Download blank image
(Right click 'Save as')