What do you mean by 'tracking'?
If the issuer reports financials, they would probably net the customers with debit balances with the amount from customers with credit balances and report a single amount on their assets side (e.g., as a receivable). i.e., it probably is such a small amount that they can report it net, and not break it out on their balance sheet.
But who knows.
Nominally there must be a significant amount of positive credit card balances if we are talking about a multi-billion dollar industry. That money is sitting somewhere. Is it literally just sitting there or does it get loaned out, put in low risk securities, or what?
I've no idea. Each time the issuer pays to settle a customer charte, that amount either comes from their capital or they borrow, I would suspect your overpayment simply means they use less capital or borrow less as a result. Maybe they put it into a separate account, ... I doubt it though.