Cheers for the info on the Synology to S3, I just had a quick look and it looks quite nifty. I will set that up once I have pushed my initial set of data up to S3 which I am doing through SyncBack. I considered quitting it and setting up the Synology to do the rest of the initial sync but I like being able to pause SyncBack if I need some bandwidth. For anyone without an snazzy Syno to do their bidding, I would recommend SyncBack Pro if you are willing to spend some cash on it. I use the Free version for transferring from this machine to my NAS and an external HDD. Works really well just scheduling it and it never bothering you again I am pretty sure the SE and Pro versions have a dropbox style setting which watches the folder for changes and does whatever action immediately.
You can do that with the Syno too. Just cancel the backup. When you restart it, it will figure out what's already been done and carry on! You can encrypt the data as well as the connection during backup to S3.