Everything is installed on the SSD. The HDD is essentially empty. The proper way to handle backups is to have a separate backup for the SSD and a separate backup for the HDD. The backups should be made to separate backup volumes or partitions.
If you use Time Machine then TM will automatically make a separate backup of each but TM does not make a bootable backup.
Get an external drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
Although you can buy a complete external drive system, you can also put one together if you are so inclined. It's relatively easy and only requires a Phillips head screwdriver (typically.) You can purchase hard drives separately. This gives you an opportunity to shop for the best prices on a hard drive of your choice. Reliable brands include Seagate, Hitachi, Western Digital, Toshiba, and Fujitsu. You can find reviews and benchmarks on many drives at Storage Review.
Enclosures for FireWire and USB are readily available. You can find only FireWire enclosures, only USB enclosures, and enclosures that feature multiple ports. I would stress getting enclosures that use the Oxford chipsets especially for Firewire drives (911, 921, 922, for example.) You can find enclosures at places such as;
All you need do is remove a case cover, mount the hard drive in the enclosure and connect the cables, then re-attach the case cover. Usually the only tool required is a small or medium Phillips screwdriver.