I have mine encrypted with Bitlocker as we speak, I use a password and I follow the latest in DoD standards which means 10+ characters, one upper case, one lower case, one number and one special mark minimum. From what I have read though it is recommend to use 20+ characters but I consider that over kill.
Once you look at cloning I would just open the folder which shows my HDD, right click and then select "manage Bitlocker". From there it will pop up a window that allows you to turn off Bitlocker. Then you shouldn't have a problem.
If you have never encrypted before I would recommend the entire drive, it may take longer but it provides extra protection.