Jailbreaking isn't for everyone. Cydia is quick to overwhelm even the tech-savvy user, and upgrading iOS software on a jailbroken device can be a headache-inducing process.
Whether you've discovered that jailbreaking isn't for you, or you need to take your iDevice to the Genius Bar for repair, you'll need to unjailbreak your device.
There are plenty of forums, blog posts, and YouTube videos that attempt to guide you through this process. Many are outdated, and, in some cases, incorrect.