I use Shirt Pocket's Super Duper to clone my working external disk to my backup disk - making sure the backup disk is offline when I start FCP X(otherwise it gets confused). This works extremely well.
SuperDuper has a 'Smart Update' feature which (when enabled) only updates files which have changed or which are new to the backup drive. Using Smart Update, the backup usually takes about two minutes per day, rather than the hours it would otherwise take.
Your backup drive must be formatted OS Extended (either journaled or not).
If I ever need the backup, I will simply rename the backup disk to be the same as the working disk so that FCP X will recongnise it.