Need Help Figuring Out How to Use/Include 1 API folder for lots of E-Commerce Websites/Templates

Hi there. I've made an E-Commerce Website and there's an API folder, which has a lot of important functions and API calls to a 3rd Party Payment company. I want to see if it's possible to keep that folder on my main system, yet include it in all the separate copies, ie. versions of the Shop Website I've made for Clients, so they can't get access to the source code, but their Shops/Sites can still utilize the functions in that folder. Really, it's about 2 to 3 files I want to protect.

I don't think I ever even change anything in this folder when I copy the code to create a new client site/shop, so it should be able to "include" somehow in all those separate installations without me having to put the actual folder into THEIR files.

Note: I can't send you the code, but I can screenshare with you, so you can see how it's setup and help me do this.

Thanks!