I too have a moral code, once when I was unloading in my car I found something in my cart that had been overlooked and I took it back in and paid for it. It was about $10.
That being said, this situation is more of a gift than something overlooked. The manager took your order and didn't charge you. It may have been his choice because you were waiting so long, who knows.
If you had noticed at the time, it would have been moral to offer payment.
Now that a day has passed, I think that bringing it up would confuse the store. Also, since it sounds like the food was neither rung in or paid for, their till would have balanced. If you send them money now, there's a good chance whoever gets it will pocket it for themselves. And they're only actually out the actual cost of the ingredients, say $1.50?
At that dollar amount, I think it wouldn't be worth the hassle.