The cover Photo is the Photo that shows when you are viewing all of your Photo Albums. When you create a Photo Album, the first Photo in the Photo Album automatically is chosen as the cover image of the Photo Album. However, you can change the cover Photo to any Photo in your Photo Album. If you change the cover Photo it will not affect the order of your Photos within your Photo Album.
You can choose your cover Photo for your Photo Album by accessing the editing screen for your album. Once you are in the editing screen you can click on the Photo that you want to be your album cover and then click on the check box within that photo's editing screen labeled “Set as album cover.” Follow the steps in the image below: