"internal s matrix" is for diagnose purpose;
"user s matrix" is a subset of the total S matrix. So when you only use it to cascade, it loses some other information. I would suggest you to find EME papers to get more details.
In your case, both will not lead to the expected result you desire. Only when you have those groups inside EME simulation can you get correct result.
You are navigating away from the AIS Discovery experience