Yeah, that can be irritating. Just open up Sonar and create a new project. Set it up the way you want, browser locations, with plugin layouts the way you want them, screensets and all that. Then save that as the "Normal" template, if that's the template you normally start with. The plugin layouts will be saved in your screensets.
Here's the bit that is a little bit tiresome - but worth it IMO: When you now open up old project and things are set the "old way", just hit Ctrl+N to create a new project, don't save it unless you want to, go back to your project and in the screenset module on the Control bar, choose import screensets from "SONAR 1" (or whatever the project is called) and then close the new project which you have no more use for. Save your own project and all the layout tweaks will remain in the project. Eventually, you will not even notice the old way as you move into new projects.
Hope this helps.