If you borrowed money from the merchant account, then it is a liability.
typically the merchant account takes some portion of your sales and applies it to the balance due, paying it down as your business makes sales.
Typically you book the gross sales, less the merchant account fee, and then you can make an entry for the loan payment.
A deposit might look like this
income, $$$$$$ (gross sales)
merchant fee expense, -$$$ (negative number)
Merchant loan payment, -$$ (negative number)
Net amount
But if you are paying an accountant, why is he not helping you make entries? he works for you, or get another one, accountants are a dime a dozen.
And what he told you to do makes no sense to me. RE is distributed to the owner(s) at the start of the year.