1. Go to http://pixlr.com/editor/ and click "Create a new image" make the size (width, height) the same as your logo spot on your website (normally 400pix by 100pix) and check "transparent" before hitting OK (the other options don't matter).
3. On the menu towards the top click "Layer" and then "Open image as layer" this will allow you to upload your logo.
4. Now select the wand tool and click on the portion you want to be transparent (such as a white background, inside font loops, etc.) then hit the Backspace or Delete button on your keyboard. You may have to repeat this step for additional sections that you want transparent.