Hi,
I guess that by "Advanced Settings" you mean setting it in SonarQube server UI. If correct, then yes you should be able to define paths there.
And for the "settings file" do you mean the configuration file of the SonarQube Scanner for MSBuild? If correct then I would not try to put project specific stuff there. My example was intended to be passed to the "begin" step:
SonarQube.Scanner.MSBuild.exe begin /k:"xxx" /n:"yyy" /v:"1.0" /d:sonar.cs.vstest.reportsPaths="%CD%\TestResults\*.trx"
++
Julien