The issue the above user is discussing has nothing to do with payments. When you import an IIF file from the Home Depot Pro Xtra website, the IIF file automatically includes a charge and a linked "payment", or credit, corresponding to that exact charge. There hasn't been any payment made. This is how the file imports. So if you go to record a credit card payment from your bank account, it will show a credit for the entire balance due on the card in your credit card account register. Further, you cannot delete the mirrored credit so that the payment you made on the statement will balance. It just deletes both sides of the transaction. 

As far as I can tell, the IIF file import is designed to make reconciliation easier by breaking apart the individual charges as credits. It just means that you cannot record a payment from your checking account or it will throw the account out of balance. Or perhaps you create a zero payment (if it will allow you to do so). 

I don't like it and I cannot find a work around for it, nor can I find anyone at Home Depot account services who can even explain this import file structure.