If you have multiple bootable backups on your external HD, you can select which one when you boot holding down the ALT (Option) key.
Let's say you have two bootable backups on your external HD called A and B. When you boot your computer while holding down the ALT (Option) key, you will be presented with all bootable partitions where A and B should show. (Note, since these partitions exist on an external HD, they will show up with an orange looking icon.) Then you select which partition, A or B, by clicking on the one that you want to boot from. Once selected your computer should boot using the selected partition.
After booting the partition that you selected will show at the top right of your desktop assuming you have your Finder set to show external HDs.