1. Tap on Cydia. It will check your file system then restart itself.
2. Tap on Cydia again, once it restarted itself.
3. It will ask you if you are a User, Developer, or Hacker. Tap User
4. Cydia will start downloading packages. Wait for that to finish. It will say "Reloading Data"
(if a pop-up asks you to Install essentials, tap "Install Essestials" This is important)
5. Open Cydia, once it's done installing Essentials. Cydia will again install release, packages and other stuff. And it will also say "Reloading Data" Just wait.
6. Pretty much the setup is complete. For how to use it, go to my post here