There are some built-in features in Sonar that really do make things easier. Templates for one (Project, Track, ProChannel), and the Plugin Manager for another. Yes, it took me a little time to set them up, but for the most part that was a one-time effort. I used Sonar for a year or two before I got around to exploring those features though.
Eventually, when the plugin list grew annoyingly long, I created a Plugin Layout in which I categorized plugins by type and by vendor. In the type folders I added my favorite and most used 'Compressors' and 'Equalizers' for example. But, since not every plugin is used very often or fits neatly into a main type, I left those in a vendor folder. The folders are sorted, the folder list is fairly short, and the lists of plugins within the folders aren't too lengthy.
You do have to manage the layouts when you add or delete plugins from your system, but I find that the Plugin Manager works well for me.