I honestly have very little experience with Kontakt, as I don’t use it!
After a quick Google search, this link to the native-instruments forum may help..
The goal of this course is about easy folder structure/file management to prevent missing files.
As I warned in the beginning of the course, you may experience missing files if you do take my advice, however, once set-up, it should prevent any missing files from there on out.
In terms of VSTs – I keep the .exe (executable download file) within my custom folder as well as the VST2 64-Bit versions.
VST3 cannot be moved, as it has to stay in the Common Files folder.