Let's say you receive an invoice for $1000 and the supplier forgets to charge you the GST. To correct this, the supplier sends you a second invoice, only for the GST.
Here's what to do.
To record GST only transactions from suppliers
Go to the Banking menu and choose Spend money.
In the Bank account field, select the bank or credit card category you're paying from.
In the Contact field, select the applicable supplier.
In the Description of transaction field, describe this transaction, e.g. "GST only on purchase number xxxxx" (or similar).
Enter the Date of the transaction, or click the calendar icon to choose the date.
In the Amounts are field, select Tax inclusive or Tax exclusive.
On the first line of the transaction:
select the required expense category
enter the original dollar amount of the expense
enter a description
select GST as the Tax code.
On the second line of the transaction:
select the same expense category as the first line
enter the original dollar amount of the expense as a negative value
enter a description
select N-T as the Tax code.
Click Record.
Note that this process will also work for receiving GST only amounts, but you'd use a Receive money transaction instead (Banking menu > Receive money).