I made a new Script folder, put all the relevant files inside, then used FOMM to BSA the folder. Didn't work, after I took out the script files from my script folder temporarily to see if it worked just going from the BSA, it wouldn't. Second attempt I made a Data/Script folder, put the script files in the script folder and tried to BSA the Data folder and followed the same steps but with the same result.
So how do you do it? It would make my mod a hell of a lot less cluttered.