I always have three copies of Beth games on SSD...
First for Creation Kit with vanilla files only or with the files for modifications over which I am currently working/checking. (together with all DLCs), second to test modifications and third for current game play.
Each in a separate directory (Fallout 4, Fallout 4 CK, Fallout 4 Test) along with INI files (in Fallout 4\INIApp, Fallout 4\INIDocs) and My custom Wrye Bash (Fallout 4\Mopy) in every directory.
I use NTFS Junction Points for all Beth games INI directory.
C:\Users\USERNAME\AppData\Local\Fallout4\ -> Fallout 4\INIApp
C:\Users\USERNAME\Documents\My Games\Fallout4\ -> Fallout 4\INIDocs
When I want to play FO4 I use "Fallout 4" directory and when I want use CK I use "Fallout 4 CK" directory.
I change the directory names
Fallout 4 -> Fallout 4 Game
Fallout 4 CK -> Fallout 4
As the directory name changes I do not need to change/edit/replace INI files because they are in every copy of the game.
I have been using this system since Skyrim (2011) which almost eliminated my problems with the stability of CK or game.
Fallout 4 Meshes...
Fallout 4 meshes are one for which Beth has provided plugin (I omit Morrowind) but as always, do it yourself and at the same time they are one of the worst done out there.
The number of people who know how how properly do meshes is small, this is due to the lack of support/guide from Beth for doing them and many guides that are wrong.
This is the result of my experience based on the analysis of several hundred meshse for FO4 (~600 modifications)
If something is not clear let me know, my English is not very good.
That's why sometimes I have problems expressing what I know/think.