If your logo has a white box behind it and you'd like it to be transparent for your cover page, you may be able to use a free online service called Lunapic.
Step 1: Upload the logo (.jpg files work best)
Step 2: Click EDIT and select TRANSPARENT
Step 3: Once the image is loaded in, select the color that you want to make transparent - typically the white "box"
Gray and white boxes are imposed over the background, indicating where the transparency is.
Step 4) Save as a .png file. Click FILE > Save as PNG