Plugin management

Hi Everyone,
I have a folder on a drive that I put all my plugins into. Within that folder are other folders labeled by type, EQ’s, Compression, etc. This is because of a former program I used. Now, with Nuendo when I open a plugin slot I have duplicate categories, the ones I created and the ones Nuendo created. The Neundo created categories seem to hold some Steinberg vst 3 and Waves vst 3 plugs. Long story short, I have double EQ, Dynamics, etc. What’s the best way to get everything organized into one folder per category. Make sense?