Edit: I totally missed that you already have an external hard drive. Here's what I wrote anyway:
Backing up to optical media is just too much of a pain in my opinion. Get yourself an external hard drive and you won't have to worry about large files spanning multiple media. Besides the hassle factor, I think it's also safer because you only have one point of failure (if just one of the multiple DVDs your Aperture library is on fails, you lose the whole thing).
You can get FireWire + USB2 cases for around $30, and several-hundred GB hard drives for less than $100 (usually after rebates).