I am a SonarQube user, currently with SonarQube 7.7 Developer Edition and have PR analysis working with Bitbucket Server 6.3.0. First, you need to have Bitbucket Server 5.15 or greater for PR decoration as the the PR integration uses the Bitbucket Insights API.
In SonarQube Server, go to Administration -> General Settings -> Pull Requests, set provider to Bitbucket Server and access token
In my sonar-project.properties, I have:
I run this through Jenkins CI (with SonarQube gating) and works great.
Let me know if I can help.