Custom Table for a Custom Post Type

I have a client with a large database of existing data for custom post types that needs to be imported into WordPress. (Formatting the data is not a problem) The problem is that the theme I’m using stores custom post types in the same table as regular posts. I want to tell WordPress to pull the data from a separate table that can be safely imported in phpMyAdmin every time that there’s an update (then nothing gets accidentally overwritten).

I’m a bit of a php beginner (I can read and modify the code all right) and I’ve never built a template, so I’m not sure where in the file structure it designates which table the data should be stored in (from dashboard) and where it pulls from (when building the page). I do know how to navigate around phpMyAdmin, so I know the post type that I’m looking for.

Can someone let me know where to start looking in the php files? Would there be anywhere else I’d need to change this? Is this all I need to do? Am I being far too ambitious?