I don't use BSA, and I have also heard they can be troublesome in a BSA. But since I do not use them, I could not confirm it.
All my objects are in special folders, so they are not MIXED in with the vanilla game objects.
Such as, objects in my Textures folder are in maker and mod named folders:
Data\Textures\WillieSea\LevelersTower\
I find this the best method for keeping your stuff separate from other mods and vanilla files.
As for the scripts, they have to go in the scripts folder. Just name then with the prefix of your mod, like for my mod Levelers Tower, I name the scripts:
Levelers***.psc
Where *** is an identifier for what the script does. Such as "EntranceDoor".
LevelersEntranceDoor.psc