Scripts can be only one folder in (I think), so I just drag and drop into a folder with it's name. For packages, I put them in a folder that explains what they do, ex. Fine Tuning (like faster restaurant cooking, slower writing books, no auto snow shoveling, More Options (such as new foods, "watching horror movies" holiday tradition), New Gameplay (ex Simda dating app, anti-fear pet training), CC (hair, clothes, etc), and Bug Fixes (such as vampire fix). That way I can find the mods easily if one goes corrupt.
Friendly reminder: Make sure to copy and paste your "saves" and "tray" folders to a non-sims related location, super important! I keep mine in it's own folder in my Downloads. Last night I was deleting some mods I no longer wanted, restarted my game, and the game had an error every time I tried to go into my last played household. Luckily I had recently backed up my saves and tray folder, and it saved the day. I have too many custom lots I've put countless hours into creating, and would have been destroyed if I had to reconstruct a new save.