FmrMSFan If you mean the CC Payment category is now red after it was $0, that is due to a return (categorized inflow), not a purchase. Additionally, TBB would have increased, so use those funds to clear the red, setting the Available back to $0. (If you already budgeted those funds elsewhere, reallocate from the lowest priority category with funds.)

FmrMSFan Is it the Credit Card Payment category or the spending category that's red and negative?

FmrMSFan Edit:  I was able to fix it.  I had recorded another purchase prior to transferring the money to cover the second payment.  I deleted purchase and the money transfer and did them over in the correct order and now it is acting as it should  The Available amount for the Amazon category is zero and the overage in the Account gets reduced as purchases are made.  Eventually I'll use up the overage, and everything will be back to normal. 

FmrMSFan Edit2:  Although the Available amount for the Amazon category is remaining zero and the overage in the Account is getting reduced as purchases are made, I feel like I'm "paying" for purchases twice!.  I moved the money to cover the second payment from my 'Cash Reserve' category, and all seems good.  However, I just made a purchase of eyeglasses for $100.35 and, although that amount was properly removed from the Amazon Account balance, it was also removed from my Medical category.  So, I've essentially paid twice.  Once from the Cash Reserve (which funded the overage) and then from my Medical category. 

FmrMSFan YNAB increased TBB when you took the account positive. Effectively, it moved funds from the payment category (turning it red) to TBB. You should have moved it back at that point, in accordance with Rule 3. If you didn't notice and put those funds elsewhere, it was money you didn't really have in the first place.

TLDR; yes, you budgeted twice, but one of those times was with fake money.

dakinemaui AH!  No it did not increase the TBB!  And yes, I understand that the first payment was fully funded by the appropriate categories as purchases were made, and the second payment had to be covered from somewhere....That's why I moved money from my cash reserve category to the Amazon category.  But at no time did the cash for the extra payment appear in TBB.  This is another reason I really, really wish YNAB had a more complete audit trail, move money log.  

FmrMSFan Guaranteed a payment that results in a credit balance (positive account balance in YNAB) will increase TBB and decrease the Payment category.

Create a new CC account and record a payment to it from checking as a quick test. Undo afterward.

FmrMSFan Think of an over-payment to a credit card like a balance transfer between two accounts. The account the money comes out of will decrease in funds, while the account the funds are paid into will increase, always resulting in a net zero change in wealth.

YNAB is another layer on top of this. When you made the second credit card payment, you either recorded, or YNAB imported, the negative amount in your checking account and a positive amount in your credit card account. If those didn't show up as a transfer, you should change them to be a transfer. Once this part is done, your TBB should be unchanged, your account you paid from should be lower by the total amount you paid from both payments, and your credit card, if you overpaid the total balance, will show a negative dollar amount available (meaning it's carrying a balance) as the difference between what you owed and what you paid.

The next thing you are doing is using your credit card to make a purchase. When you purchase something, you assign it to a spending category, not directly to the credit card. For example, clothing bought on the card would be assigned to a clothing category, and YNAB will apparently work it's magic, recognize the payment occurred on a credit card, see that the credit card has a positive balance, and make no change to the budget category.

However I think it depends on whether you're making the cc payment in the same month that the over-payment occurred. Right now I have a positive balance on a CC that I over-payed, and I have no budget, no actuals, and no available on the cc category because the over-payment occurred in a previous month. YNAB will see that cc balance just like it would a checking account - as dollars that are allocated to something in your budget. This means, when you spend from the over-payed credit card in a category like clothing, the balance on the credit card would go down - much like if it were a checking account - and the available amount in the clothing category would go down as well. Because you spent money.

If, on the other hand you make the credit card purchase in the same month you over-payed, YNAB will basically do the reverse of what it does when you charge to your card and incur a debt. It will recognize that you made a purchase to the clothing category and effectively transfer that same amount from the available credit card spend to the clothing category, which remains unchanged. Within that same month, the CC available amount will show as negative in the amount you overpaid.

I think the missing link is in the monthly rollover. At that time, I believe, the negative available amount on a credit card that's overpaid is rolled into TBB so you can allocate it out to other categories.

Edit: made about 1 trillion edits. But I'm done now.