First of all, congratulations on having two drives and backing one up to the other. This puts you way ahead of most of the world.
Second, I would suggest that you do a quick Google of "backup strategy" and scan some of the articles that you find. There are many software packages and many strategies depending on how hard you want to work and how critical it is to you not to lose anything / stuff older than a week / stuff you entered today.
A general suggestion: Choose backup software, buy (!) and install it, and run it on a regular schedule. Disconnect the backup drive from your computer except when you are running backups, so that a power surge or successful virus can't wipe it out.
I'm currently using MirrorFolder for my most critical realtime files - mainly my Email folder. It provides driver-level Raid1 for specified folders, so every write is backed up to a secondary drive (which obviously can't be disconnected, as above, most of the time). It also allows periodic syncs of folders to a backup drive, or can be used on-demand if you disconnect your backup drive. Everything else, I backup about weekly to an external drive which I then remove.
If you let me know what your tolerance for losing data is (none, everything I put in in the last week, one day's worth of work) I can make more concrete suggestions. I deal with almost every level of paranoia in backing up, including offsite copies. For example, data that I need for court reports is backed up from my home computer to a USB key on my keychain. Onsite backups are useless if your site is destroyed or unavailable.
(This is a bigger question than "what system should I build. Really.)