Cats and kittens are very odd about how they want to be scratched. Most don't like to be handled rough, but I had a cat named Strawberry once who would only purr when you basically grabbed his skin and tugged. He liked to be scratched HARD. It was weird, like he had less nerve endings or something.
The rest of my cats hate fingernails (probably because I don't have any and I pet them the most.) Some of them like to petted very softly with a hand running from their head to their back. Some like to lay on their back and have you scratch their chest and stomach. Some won't let you touch anything below their neck.
Basically, your cat will let you know! I'd say the best practice is to try everything once. In my personal experience, I've noticed that short haired kitties deal better with rougher scratching. Perhaps because their fur is denser? Who knows..