The folder structure is pretty straightforward: hak files go in the hak folder, mod files in the mod folder, tlk files in the tlk folder, etc.

Thanks for reply - but I find it inconsistent for the important stuff, sure though - plopping stuff in override is easy enough - but HAKs - patches and more serious modding of the game is all over the place - for example, Community Patch 1.72 by Shadooow:

HOW TO INSTALL COMMUNITY PATCH 1.72 INTO NWN:ENHANCED EDITION

1) Copy content of the folder "copy into game's user folder" into NWN:EE user folder - this should be ~/Documents/Neverwinter Nights but cany vary based on OS. This action should not require to overwrite anything (unless you installed 1.72 once already).
2) Copy content of the folder "copy into game's installation folder" into NWN:EE installation folder - the default path for windows is ~/Program Files/Beamdog/00829/ but can vary based on OS. This action *should* require to overwrite some of the files, allow it. If it didn't you are in wrong path. Also note that you might need admin permissions if NWN:EE is installed into Program Files.
3) Start NWN:EE, you should notice a 1.72 "sticker" below Hordes of Underdark logo and you should hear original NWN theme music in menu.

BeamDog client should not force an update on you, however when new headstart version will be released, re-installing this package will be needed.

On top of that - the Linux (native or proton) game file locations add some variance to the mix. In the case of the Community Patch - stuff gets placed in both the Installation and User locations.

Now, if you use Steam Workshop to add stuff - their file structure works in some other fashion but mimics the actual user structure as far as I can tell.

The nwn.ini file found in " documents/Neverwinter Nights" gives you the option to define where what goes yourself.