When you uncheck the box the upper right hand words change from Invoice to reference no. You would be using this  if you have inventory and the items have come in  or been received but you are still waiting on the invoice but you want your inventory to be updated to actual amount in stock. You would use the packing slip number for your reference number and instead of choosing " invoice" in upper left side choose "Goods received note" ( you will have to set up a linked account for your inventory)  then you fill in your order  or you put your po number or quote number in the "order/quote no" field. this will bring up  your order and you can enter items that came in under the received column on the invoice. this will update your inventory.. then when you receive the invoice, you would put the reference number in the GRN/order/quote no field and it would bring up the Goods received invoice and will be all filled in. you just have to put in the invoice number ! Hope this helps you to understand!

Thank you so much for explaining that to me!!