The most important thing is that the samples (.wav, aif, ncw and so on) are in the right relationship to the file that you are loading. Other formats work in a similar manner.
A basic nki/nkm contains information about where to find all the bits and what to do with them. So if the nki file expects to see 117 files in a certain place and they are not there, it will point that fact out and show you where it thinks they should be. If you know where they are, you then re-direct Kontakt to the right place.
Normally, when you download a zip it will contain at least one nki file and the samples that come with it. If the author has followed routine behaviour, the files will be in the proper relationship in the unzipped folder.
NI’s own libraries will install into some obscure but fixed folder, in the hope that users will not move them and cause the chaos that usually follows (projects don’t load, it normally involves a lot of frustration and reinstallation of all the libraries).
Personally I have my hard drive partitioned with C:/for the Windows System, main programmes and basic stuff. Partition D:/ is for mainly for Samples and Patches that I download that don’t automatically install elsewhere.
My main folders are categorised by format primarily, the exception being the 170GB Pianobook folder which is in the nki/hkm folder and has everything in there from exs, decent sampler, sfz and kontakt formats sorted as on Pianobook. But that needs trimming right down.
So everything from Pianobook is in;
D:Samples and PatchesnkiPainobook
If your libraries have an installer and put things in certain places, make a note of the path(s) so you can find them later. Where the plugins or patches don’t automatically install and are as-is (like Pianobook downloads), takes notes and keep them away from Windows system files and your DAWs folders files.
Be sensible, know from the get-go where everything is, where it goes and why. It might be a bit confusing at first, but it will become second nature.
Finally, one last tip, I work with every file showing the file extension. If you don’t see .nki or .wav or .aif after file names then you have the option to show them as follows.
Open any folder, and click on the View tab at the top. To the far right you should see Options, click on the dropdown arrow and then select Change folder and search options.
In the dialogue box for Folder Options, click on the View tab and untick the box that says; Hide extensions for known file types
Close the dialogue box and look inside a folder and the files extension will now be displayed.