Individual Schema data ingestion from two different source

Hi @gprime84  - 

I recommend to create a separate schema for each external system to make the proper profile stitching and unification from the different external system ( Assuming both are external system with different data source and meant for unifying the customer profile). Make sure you have the primary identifier on both the external system to identify the user and make them in to the identity graph as a single customer.
Have a look on the below document for your better understanding on the identity graph and it purpose : https://experienceleague.adobe.com/docs/experience-platform/identity/namespaces.html

As you mentioned, System2 does not have the system1_id id and vice versa, then unification and profile stitching not gonna happen unless the both the schemas have primary identifier. Otherwise, both those external system data live in separate silos under AEP data lake. Therefore, strongly suggest to revisit your schema creation, create required identity namespace, apply the necessary primary identifier accordingly. 

Hope, I made it clear and let me know in case if you have any clarification.

Note: In case if you create the single schema for both external system then you would be able to assign only one primary identifier and there are other complication while you work on the data preparation. I also don't think so you can utilize single schema for the multiple dataset on this specific scenario.