I'm looking for best practices using SonarQube with the FindBugs, PMD and Checkstyle plugins.
The SonarQube Java plugin alone already covers all the Checkstyle and PMD rules - which is why the related plugins are no more bundled in SonarQube. So you can get rid of those plugins and forget the related rules.
Concerning Findbugs, most rules are complementary to the SonarQube Java plugin rules. There's no "Sonar way with Findbugs" profile anymore because that's the convention for all the language plugin to have only a "Sonar way" profile.