“The E. P. only had effect in the North since the Southern States had succeeded.”
What? This makes no sense. Unless by “the North” you mean whatever previously rebellious territory had been conquered by the North.
“So, I think your premise is correct - he only freed the slaves in the North.”
Again, unless you have an idiosyncratic operational definition of “the North,” no, he didn’t. He was expressly forbidden by Dred Scott from doing so.
The Union - the United States minus the Confederate States of America - the ones who wore blue - the part that used the American flag.
He had no legal authority to free any slaves in the Confederacy.