Obviously different versions of the requirements need to be downloaded and installed.
Refer to the Installation Instructions.
Use the -m, -p and -d command line arguments to set the INI, plugins.txt and Data paths when starting the tools. For example:
-m:"c:\Users\[USERNAME]\Documents\My Games\Skyrim Special Edition GOG\" -p:"c:\Users\[USERNAME]\AppData\Local\Skyrim Special Edition GOG\plugins.txt" -d:"c:\GOG Games\Skyrim Special Edition GOG\Data\"
Replace [USERNAME] and the INI and Data folder paths accordingly for the actual setup.
Do not link to files or folders in mod manager profiles. Link to the files and folders used by the game.