You should also have a look at the basic SSD optimisation guide for Debian (and friends). It's an added level of redundancy and an extra 1–7 day backup¹). When I'm at home, I plug in the second disk and let the md device synchronise. The rest of the HDD is one of two members of a RAID-1 setup, with one disk usually missing. My laptop is running on a similar layout where /, /usr and /usr/local are on a RAID-1 device across a 64 GB SSD and a 64 GB partition on the 1TB HDD, and the rest of the filesystems are on the rest of the HDD. You get the best of both worlds (almost), and you don't have to worry about SSD wear rendering your data useless. It'll write to the HDD, but handle SSD writes with care to avoid wearing out the device. The kernel will read mostly from the SSD (with occasional, brief forays into the HDD to increase read throughput even more).
The filesystems that would normally go on the SSD alone can now go on this md device. It'll walk you through setting up md(4) devices with your SSD as a ‘mostly-read’ device (fast reads, fewer writes), your HDD as a ‘mostly-write’ device (no-wear writes, fewer reads). Since you have two disks, though, you can read the Multi HDD/SSD article on the Debian wiki.