You’ll most likely (if you’re wise) use borders to keep your stockinette stitch from rolling. Borders keep things from stretching, too. This is because different stitch patterns stretch different ways, so when you combine them, it keeps stretching to a minimum. A border around the entire blanket will help, but I would think that borders around individual squares in conjunction with a border around the blanket would be even better.
Some common border stitches include garter stitch, seed stitch, and moss stitch. Seed stitch and moss stitch are very similar looking, but I find seed stitch easier since you don’t have to keep track of rows. I suppose you could also use some form of ribbing for a border, but that might give your afghan more of a sweater feel. If you’re not familiar with the above mentioned stitches, you can search for them online and see what they look like and how to do them.
I admire your ability to tackle such a large project. Here’s wishing you tons of inspiration to carry you through, and I hope you’ll show us not only your completed project, but also some of your progress along the way.