If you are just using it as a backup there is not much advantage in partitioning the drive, it just adds more layers to hunt through when reinstating data.
As to cloning, yes! And yes again! I keep my program and system files on the first (small) partition on my C drive and clone that regularly to my external usb disk using Acronis True Image. I keep the last 3 clones and delete the earliest ones when adding a new one. Doesn't take long and will work in the background. Can be useful if you have installed a program which gives problems. Saved me once when I caught a virus which I couldn't shift - just restored the last clone. Because I keep all my data on the second partition on drive C the inconvenience is minimal.
You can also use Acronis (or similar programs) to create clones of your data folders but, to me, the slight saving in space is not worth the extra time taken to clone/ recover the files. Just drag the folders onto the external drive. If you want a file you can go straight there and use it directly without having to run a recovery program.