If you unplug your external hard drive, it will just pause any downloads you had set. When you plug it back in it should start backing up again. I have all my files on my external drive and that is what is backing up for me.
I know they upgraded, and I have not gone into the new settings. I just put a check mark on everything I wanted backed up and it does it automatically now, but I am done with my initial backup.
They are great at replying to you quickly with any questions, and they have a lot of answers on their website.
Good luck. I think you will be very happy with them. I have been. Did you find a coupon, I hope!