Let me help you in resolving the credits, kaneika.
The most possible reason why you can see a credit because the fee was added on the invoice and the payment is still equal to the original invoice amount.
We can fix the credit by removing the fee you've added on the invoice. Then, you have two options to record the fee. One is to include it when you make a deposit. That way, you can match it with the transaction in Banking. The other option is to create an expense transaction. However, you won't be able to link it to the invoice.
These are the steps to make a deposit with the fee:
You can now match it to the banking page. I've added links for your reference:
Please post again and tag my name if you need more help. Have a great day!