Will using uninstall programs in Windows harm anything, or should I do it manually?

I'm not sure what you mean by "uninstall programs." Are you talking about a 3rd party program?
 
Anyway, this is the official method of cleaning house.
 
https://www.cakewalk.com/Support/Knowledge-Base/2007013372/Clean-Install-All-Cakewalk-Software

I meant "add remove programs" in Win 7. Thanks for the link.
 
I don't want to remove Platinum.

The cleanest way is to remove them all, then install what you need, oldest to newest if you want to keep more than one version. 
 
But you also may need to consider that the Sonar programs and features do not take much disk space.   Leaving them in place is the easy way.  Some plugins that you may have used in projects are not always available in the latest version of Sonar. 
 
The missing plugins can be recovered after installing the latest version of Sonar, by running the previous Sonar installers in advanced mode and selecting only the plugins you wish to install, while skipping the program files, etc.

If you use VVocal keep X2 or X3. It's the only "plugin" that is tied to the actual Sonar".exe. You must keep either one installed.

V-Vocal is not really "tied" to the exe, it is part of the minimal SONAR install. After installation it is possible to manually remove everything except the V-Vocal folder and the plug-in will still work.

on the installation side you need to allow the Sonar Exe to install to get VVocal, which I though appropriate considering the last line or two of the post before mine. Just trying to keep things simple.

Unless you really really need the disk space I would advise against uninstalling them at all. You may lose plugins and features that are tied to those Sonar versions. The older installations don't really negatively affect the performance of Platinum and even the program folders on disk don't take up that much space - the shared content is by far the most and you won't be deleting that anyway.

Yeah, I'm starting to think just leaving everything would be best. I'm not having any issues, and it sounds like I may create some for myself if I start messing around to much.

If you are looking to free up space and installed the tutorials; consider deleting them. Here is a breakdown of X3 disk usage I did a while back http://forum.cakewalk.com/FindPost/3179366