To reiterate Hodders you need to take into account redundancy and backup.
Redundancy
If a hard drive goes pop you want to be able to swap out the broken one for a new one without losing data and without much hassle. There are a few ways to do this but it always means duplicating data, so if you want 6TB of storage you'll probably need to buy 2 x 6TB drives.
You could buy yourself a NAS unit and set it up with RAID 1 (or 5, 6). This mirrors your data across two or more drives. I've never owned a NAS so I'll let others talk of the benefits of this.
I personally use drive pooling software (e.g. Drive Bender, StableBit). This allows you to combine the capacity of multiple hard drives into a single large storage drive. For instance 3 x 4TB drives would appear as 12TB. You can then enable duplication where a hidden copy of every file is stored on a different physical drive. If a drive fails, insert a new one and it can be populated from the hidden duplicates. This of course means that each files takes up twice its file size, a 5GB file will use 10GB of space.
Backup
Redundancy is great for if a hard drive fails but it's useless if your house burns down or if you accidentally delete something you later need.
For my important documents and photos I use cloud backup (e.g. crashplan, backblaze). This software sits in the background and continuously backs up changes to your data. This means you can restore data from any moment in time. Crashplan lets you back up for free to another computer with crashplan installed (e.g. to a relatives PC) or to their cloud for a paid subscription ($5/month).
There are lots of ways to do this, that's how I did it
And finally, to answer your original question buying 2 x 3TB drives may save you ~£20 over buying 1 x 6TB drive, but for that little difference I'd always prefer having the higher capacity to keep my case less crowded.
