As most may be aware, SKSE has undergone some 'revisions' of late. Such as preload, crash fixes, etc.
While trying to make all this work in the context of Mod Organizer, I was ending up with three separate installs -SKSE, the memory patch, and the crashfix. When finished, upon launch I always got a msg about not having memory configured correctly. (Of course, I had commented out the entire memory section per Sheson's newer instructions)
In the end, I made a 'data' folder, and under that a 'SKSE' and a 'Scripts' folder. In the SKSE folder I added the modified SKSE.ini file, made a 'Plugins' folder, and into the plugins folder I added the three crashfixplugin files and the two memoryblockslog files.
I then copied over all of the scripts into the scripts folder (including the 'src' folder, just because...)
Finally, I archived (I use 7zip) the 'data' folder with all of the above into a 7z file that I called (DUH!!!) SKSE. Mod Organizer installed this justfinethankyou, and no more nasty grams about memory issues. There may be issues down the line with mods that also add plugin files, (PapyrusUtils comes to mind), but we will see.
Any comments on where, how or if I went wrong, please feel free.
In my defense, I am returning to Skyrim after a significant absence and I have never used Mod Organizer til now.