The AKC is the original, well known registry. A few years back, the AKC adopted new, stricter requirements like DNA testing and kennel inspections. As a result, many breeders were suspended or could no longer meet the requirements to register.
A bunch of "alternative" registries were formed for the breeders who couldn't qualify to register with the AKC anymore. Many breeders who use these alternative registries claim it's because it is cheaper, but that's just smoke and mirrors. The AKC requires breeders to prove that the puppies are purebred and the papers are accurate with DNA testing. The CKC only requires you to have two people who aren't experts (could be your best friend or Uncle Harry) sign a piece of paper saying your dog is a purebred. If you submit that piece of paper and three photographs of your dog, they'll take your word for the fact he is a purebred ..... provided, of course, you don't forget to send $12.
As far as selling puppies, a careful person will thoroughly screen breeders and a registry other than AKC will be a red flag.