Need advice on how to setup a production server

I have a server at home and installed erpnext but i as i understand i cant modify it as it will not allow me to update in the future. What is the proper way to make a private repo for my own version of erpnext? Will creating such repo break the auto install script?

Make an independent app for your customization. Store in git dor future pull. Don’t touch Frappe or ERPNext core. This method ensures that update doesn’t break your instance.