The cover photo of an online album is determined by the first photo in the album.
This means that you can change the cover photo, simply by dragging the the photo you would like to have as the cover photo to replace the first photo, which is at the top left corner of the photos in the album.
Please note that if you are using the Family Tree Builder to edit your tree you will not be able to change the order of the photos online. You will be able to do so however in the Family Tree Builder, under Photos > Albums. Click on the album you would like to reorganize, and drag the photos to the correct place in the photo list.