From how I understand it, the invoice or bank payment is entered in the usual way entering the net amount with the appropriate tax code. You then select the prepayments option on the nominal ledger tool bar and this is where you break down the 3 months' instalments and you do not need to break down the Net/VAT amounts in this part, but by entering the N/C for rent and the prepayment N/C this will action the necessary postings for Dr and Xr Prepayment/Rent.
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