I just booked a couple Rapid Reward (older Rewards) on the website a few minutes ago. If you can see your award, there should be a tab that says something about "Book Award Travel" or something like that. Keep poking around, you'll find it. If not, then just call.
I have the certificates too. I got them through the Rapid Rewards credit card promo. I see them in my RR account but can't book any flights online. It's impossible to get through to SW right now via the phone seeing as they just changed over the RR program and everyone has questions! ARGH! Any advice?