Mind if I jump in?
Hi Peter - this particular issue came up internally about a month ago. We have been looking at the whole area of bank explanation, including unallocated cash, payments on account, paying off credit notes and dealing with adjustments for forex, commission & bank deductions etc in an effort firstly, to bring in functionality previously missed, and secondly to make the processes easier and more intuitive. So all I can say, at the moment is watch this space.
In the mean time, if you want to leave the credit note in situ, say because it's been VAT returned, then the best route is to raise a dummy bill for the gross amount, outside of VAT, putting the cost to say suspense (or where the original cost & credit note ended up) and use the credit note to pay it off. Then post the bank receipt, as a transaction, again outside VAT, to the same account code. If the account code is not visible from the drop down list then you'll need to tick the "Show in Sales" check box in the Codes list.
Hope that helps
Cheers
Paul