Couple things:
-- Please don't consider a 2nd HDD as backup (i.e. reliable storage meant to safeguard important data). It really functions as redundancy, i.e. the data remains readily available in the event HDD1 crashes. IMO, it's not really safe enough for proper backup. For example, the same root cause of one HDD failure could cause both HDDs to fail simultaneously. FWIW, here's a
description of my redundancy / backup model. And here's a post I made on "
reasonable redundancy withour RAID" that you may (or may not) find useful. I strongly recommend a proper backup on a less volatile / risky (if properly stored) media, like optical (e.g. DVD). The same root cause of data failure for a HDD is unlikely to render optical media backups unusable. Though it is possible: fire, flood, etc. Which is why you should always have an off-site backup, as well.
-- If you can afford it, use 3 internal HDDs to separate your OS and programs from your data: one for OS and programs, a 2nd for data only, and a 3rd for data redundancy. This makes re-install of or upgrading your OS and programs less risky to the data. Alternatively, you could use 2 HDDs and partition one HDD to achieve a similar effect: HDD1 has 2 partitions - partition "C" for OS and programs, and partition "D" for data. If the OS bombs, you re-install the OS and programs partition "C", without impacting partition "D". The downside of the partition route is that the space available for data on HDD1 will be smaller than the space available for data on HDD2. But when you're talking a 1 TB drive, carving out an 8-12 GB partition for OS & programs probably isn't a big deal.