Thanks @doug_pantheon and @alex, the site is Drupal 8.
I think I’m confusing myself here which is not helping with my explanations.
I ran through the guide on updating a custom upstream - I created a new site to test with, I checked out my upstream and I added the contrib modules I needed and I also updated Drupal core (maybe I shouldn’t have done this?)
Then, in my test site I committed all changes and config but when trying to import config on multidev I get a lot of errors about entities existing and mis matched site UUID. This had me thinking that maybe the config should not be in the upstream ?
I guess my main questions are;
Does the custom upstream need to have Drupal updated in it? Or do I just pull from the pantheon upstream to manage that?
When adding contrib modules and making any config updates, do I add them to the custom upstream?
This is not a problem with docs I dont think, I 'm just having a hard time getting my head around the flow and process.