@TasteOfGraze 

"I remember only enough from my college accounting classes to make me not look like a complete idiot."

If that's all it takes for you to keep from looking like a complete idiot, you're doing great.  I often look like a complete idiot.  

If deleting the payment throws off your cc reconciliation, then you must have entered the original cc charge.  Is that correct?  If so, what account did you assign to the charge?  The second payment that you entered from the business bank account - did you ever actually make that payment to the cc or not?  Was that the journal entry you're referring to?  Was that a debit to the cc liability account and a credit to the business checking account or ???

If I'm understanding that correctly (doubtful), and the original cc charge was recorded in QB, you will need to reverse that entry.  That entry is a debit to the cc liability account and a credit to the same account as the original charge.  That will replace the cc payment that you deleted and should get your beginning balance back on track.  Let me know how much of this I'm not understanding correctly.