Here’s what I wrote in another thread:
I use 3 VST top-level paths to organize my plugins.
Cubase 64 uses VST_Plugins_64bit_only and VST_Plugins_32_64
Cubase 32 uses VST_Plugins_32bit_only and VST_Plugins_32_64
So if a VST comes with both a 32-bit dll and a 64-bit dll they go in VST_Plugins_32bit_only and VST_Plugins_64bit_only respectively.
If a plugin only has a 32-bit dll and that dll works fine in Cubase 64 it goes in the VST_Plugins_32_64
If a plugin only has a 32-bit dll, but it needs to be JBridged to work in Cubase 64, then the dll goes in VST_Plugins_32bit_only and the JBridged version (which references the 32-bit dll) goes in VST_Plugins_64bit_only
If I have a memory hogging VST that has a 64-bit dll, I can put the dll in Cubase 64 uses VST_Plugins_64bit_only and then put a JBridged verion (referencing the 64-bit dll) in the VST_Plugins_32bit_only and use it instead of the 32-bit dll for better memory allocation when running Cubase-32.
With this setup I can open my projects in either Cubase-32 or Cubase-64. Normally I use Cubase 64, but there are times when I need to use Cubase 32.
I use identical sub-folder structures under each so that they are organized properly in the menus.
What I didn’t expand on was the last sentence about subfolder structure. I actually have 6 paths not 3 as stated above to separate Instruments from plugins (i.e. VST_Plugins_32bit_only\instruments, VST_Plugins_64bit_only\instruments, etc.). Just my preference. So below instruments I would have the following subfolders: Drums, Synths, SamplerPlayers, Pianos, etc. These subfolders are identical across the 3 VST_Plugins_32bit_only\Instruments, VST_Plugins_32bit_only\Instruments and VST_Plugins_32_64\Instruments. This way my menus are all organized. No problems with whether they are bridged or not.
The only real issue are VST3s, which provide no mechinism for organizing.