Short story: for most VSTis the VSTi *.dll file does not have to be in the same folder as the samples. Once the VSTi is properly installed, authorized and registered, if you move the samples, when you load the instrument it will tell you it cannot find the samples and ask you if you want to browse for them … or some other such similar question/ option. As long as you remembered what directory you placed the samples into … no problem.
Most VST/ VSTi plugins themselves can be moved somewhere else later if you want … although there are a few exceptions that require keeping them in the installation directory for proper operation.
Most people place their VST2.0 and VSTi2.0 in the windows program directory … slightly different depending on which version of windows you use … Steinberg>vstplugins. This is just for convenience, since many plugins use this as default for installation. But as long as you can point the program through ‘preferences’ to where the VST/ VSTi folders are located on your system, you can place them where you want and have as many subdirectories as you want.
I like to use a different subfolder in vstplugins for instruments and effects. Then inside the effects folder, for example, I have further subfolders … for examples one for EQs, one for Compressors, one for Delays, etc.
The VST3 plugins are set in a default directory by Steinberg and 3rd party manufacturers use that same directory address.
There you go … a mini course on VST/ VSTi handling.