I know PCs like the back of my hand blindfolded, and hopping on one leg whilst balancing china plates on the edge of my nose (or something similar).
As to your issue....
Have a look at a piece of s/w called Acronis True Image.
For what you are trying to do, this will suffice your needs perfectly.
It will snapshot your current OS HDD into a single file, and more importantly it will do whilst you're logged in to it (other backup software sometimes asks for you to be going from a DOS type prompt).
No need to partition your HDD, though if you wanted to keep multiple backup versions (dates), then you may want to divide your external storage either as drives, or more simple by creating folders.
If you need any more help let me know