How to inform the editorial office that a special discount has been received?
From the details given in the question it's a bit hard to tell what exactly happened. Still, my read is that the journal is accepting papers for both the special issue and regular issues. You're asked to contact the editorial office to identify your submission as part of the special issue, since otherwise they wouldn't know how to tell one from another. So you write something similar to what you wrote in the question: I'm submitting this article that's part of this special issue, and I'm told there's a discount applicable / free.

On a side note, it's unusual to me that you're asked about payment upon submission, since usually payment only happens upon acceptance (and then only for open access articles). You might want to check if the journal is a genuine one.