hi Phelec
Try this.
You will need to create a new account in either assets or liabilities called 'Quote clearing account' with the tax code GST. In items you will need to create a new item that you sell maybe called 'Invoiced', Income account for tracking will be the new account you created 'Quote clearing account', with the tax code being GST. You will get a warning about the account you are using but just okay that.
Do your item quote up with all items entered and add some identifier maybe the quote number that comes up automatically but something slightly different, maybe IQ before the number or after.
Then do your quote that you do for the customer and send this to them, but allocate this Quote to the Quote clearing account you created and make sure the quote number is the same as the detailed except without the IQ.
Once the customer accepts the quote, convert both to an invoice. On the itemised one prior to recording it go and add a line of -1 then the item Invoiced and then enter the total amount of the invoice in the price column.
When i tried to this 3 times, the system did not like it and kept saying something went wrong, so i just converted it to an invoice and then went back to the itemised invoice and added the line after it was converted.
This will keep your inventory stocktake correct.
Let me know how you go.