Bare with me as I'm still new to Sonar. I thought I'd mash my questions up into one thread to keep things organized.
 
(Solved this thanks to scook) To start off, I was wondering if there was a way to organize or unify all plugins to one folder/list. At the current moment it's a little messy having to go through different folders just to access a plugin.
 

 
Next, is there a way to have Background Color follow the Track Color? I know the Foreground Color will follow the Track Color if I select the "Use Track Colors" option in the Clip Properties. I'd like to have the Background Color follow it instead so that my tracks look something like the following image without having to change both Track Color and Background Color, because that's time consuming if you happen to have a decent sized project.
 

 
Finally, how have you guys on X3e been working around the Vertical Zoom issue. Maybe I simply have anger issues, but it ticks me off after a few minutes of having to scroll back up in a project every time I use Vertical Zoom.

It is possible to create custom plug-in layouts. Click on the down arrow next to Plugins tab and select "Manage Layouts..." Keep in mind, once you decide to use custom layouts, you must maintain them when adding or removing plug-ins.

Clicking on "Manage Layouts..." doesn't seem to do anything. I'm not getting any popups or windows following selecting it.

It should launch the Cakewalk Plug-in Manager populating the layout panel on the right. Make sure it is not hiding behind SONAR.

It isn't hiding anywhere, it isn't launching anything.

The Cakewalk Plug-in Manager may be run from the Utilities menu. Not sure why it does not launch from the context menu. If you are not running SONAR as administrator, you could see if that makes a difference.

I was able to launch it through the Utilities. Thank you, I appreciate the help.

Anyone know about the other two questions?

I don't think the background color thing is possible. I agree with you though, I'd prefer background color be the color indicator because there's more of it and audio data is then kept equal: it's always black. 

I just recently upgraded to X3 and I also spent a long time changing each track color to follow the outside clip color. I prefer my waves drawn in black on top of a lighter clip color, so I would definitely like to see an option where the background color follows the track color. Maybe something for the next update?