This is probably going sound dumb, but were in my Arcanum program files, would I place added and changed scripts?
If you unpack the Arcanum4.dat (patched game) you'll find the dlg and scr folders. Otherwise you simply create new dlg and scr folders in your Arcanum/Modules/Arcanum folder and add your scripts there.
If you want to add changed files to the Arcanum mod, make a new folder in your Arcanum folder that is "sierra\arcanum\data" and inside that folder, you use the same structure as is used in the .dat files. So if you want to add dialogue files(.dlg), you place them in the "arcanum\data\dlg" folder. From what I gather you want to add a modified script, I'm not sure whether you mean an actual script file(.scr) or a modified .mes file. Generally if it's a .mes file place it in the "arcanum\data\rules" folder. If it's a .scr file place it in the "arcanum\data\scr" folder. If it's a mes file and placing it in the rules folder doesn't work, you should probably try the "arcanum\data\mes" folder.