Trying to clean up my older 1.3.7.1 site in preparation for upgrade.

I have a lot of files that are within overrides, but not consistent.
So, here's my question:

If I have a file that was from an add-on and doesn't exist in a standard folder, can it exist ONLY in the override folder and work correctly?

While looking through my folders, I see some add-ons are in the (example) includes/languages/english/modules/order_total folder, while others are in includes/languages/english/modules/order_total folder/CUSTOM folder, but NOT BOTH.


thanks,