Initial back-up for Yosemite X10.10.2

I bought my first MAC before thanksgiving and am wanting to properly back up my hard drive to an external source. How do I set up my machine to automatically back up my data on another partition while backing up my system and program information on a another partition? I already have to try and fix an issue with filevult not being able to fulling install, so I must back up the information and have a good system restore. These actions are all new to me on a Apple. I want to make the initial backup the correct way the first time. Below are my system properties.
MacBook Pro (Retina, 13-inch, Mid 2014)
OS X10.10.2 (14C109)
2.8 GHz Intel Core i5
16 GB 1600 MHz DDR3
500 GB flash memory HD
I have one two-TB external hard drive (WD My Passport Ultra) that I need to use on both Windows and Mac.
Thank you very much for your help.
-todd

Why back up to 2 different places?
Time Machine Basics
Time Machine Basics (2)
Time Machine Versus Clones and Archives 
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