The old coot that used to run the Oregon Leather Store in Portland was full of advice when I went buying my first tools, and he said "Ditch the rivet tool and just hammer the darn thing flat. Looks just as good on those silly Rapid Rivets and it's a heckuva lot easier.". I've been using that method ever since. I occasionally get one crooked, but mostly it works. I keep a light hand for the first hit, and then a firmer tap on the second to make sure it set. Don't smack it too hard, though, or you'll pound it TOO flat.
the comments above about making sure you have the correct length are spot-on though. The Rapid Rivets will kinda 'snap' together before you set them. If it won't stay connected once you let go, the stem is too short. If you can see lots of air gap between the cap and the leather, the stem is too long.
If you're out of the right length and the one you have is a tad short, one solid tap on the hole with a ball peen hammer will compress the leather long enough for you to set the rivet and it won't look too bad.