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How do I "explain a transaction" as: "a payment of an invoice"

It seems the default explanation for transaction types is, "Refund". However if a credit is a payment from a customer, there is only one possible selectable type for it, "Other Money In". But using "Other Money In" won't account for VAT, will it?

I assume that I shouldn't be using the category, "Misc Income Receipt" for customer invoice payments. And since in my case customer payments by credit card won't actually be the amount shown on the invoice to the customer (due to per-transaction processing fees removed at the time of transaction), I'm struggling to see how I can use FreeAgent to do the bank reconcilliation.
 
sad I’m bemused
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