To fully take advantage of SonarQube in Eclipse, it is recommended that your project is already being analyzed on a regular basis by SonarQube. Indeed, you'll get features such as only displaying new issues that you have introduced.
However, if you want to give SonarQube in Eclipse a quick try, you just have to first declare your project through the SonarQube web interface.
Setting SonarQube Servers
Go to Window > Preferences > SonarQube > Servers.
SonarQube in Eclipse is pre-configured to access a local SonarQube server listening on http://localhost:9000/. You can edit this server, delete it or add new ones.
Linking a Project to One Analyzed on a SonarQube Server
Linking for the first time
Once the SonarQube server is defined, the next step is to link your Eclipse project with a project defined on this SonarQube server.
To do so, right-click on the project in the Project Explorer, and then Configure > Associate with SonarQube...:
In the SonarQube project text field, start typing the name of the project and select it in the list box:
Click on Finish. Your project is now associated to one analyzed on your SonarQube server.
At any time, it is possible to change the project association.
To do so, right-click on the project in the Project Explorer, and then SonarQube > Change Project Association...:
Unlinking a Project
To do so, right-click on the project in the Project Explorer, and then SonarQube > Remove SonarQube Nature:
Additional settings (such as markers for new issues) are available through Window > Preferences > SonarQube:
You are now all set with configuration and you can start using SonarQube in Eclipse.