The current binding process requires that each Eclipse project to be bound to the correct module on SonarQube side. It also doesn't support if the Eclipse files are located in a subfolder of the remote SQ project.
We will change this behavior. Users will only have to choose the correct SQ project and we'll do our best to locate the matching files (they could be in a subfolder, or in a module).
This will also prepare to the upcoming drop of modules on SonarQube server side.