We have that same issue. The batches don't necessarily match up the day they are posted...or the fees are taken out.
So we do a monthly reconciliations. To get started, the company that processes your credit cards should be able to provide you with a monthly statement with the batch numbers. It may have to be something you request.
But then we created a spreadsheet where we downloaded all of our bank transactions and then downloaded the credit card transactions. Each carrier has a specific percentage fee. So you can figure out how much the fee was based on the transaction. You should also have a POS (point of sale) transaction that shows person X bought 100.00 from you. After the credit care fee you may only see $97.00. So you can match up the 100 with the 97 and have a $3 entry for Credit Card fees so the 97 + the 3 = 100 from your POS