Yes, you can enter a negative amount on your invoices. I'd be pleased to walk you through how to do that.
The system requires you to enter an amount that is greater than zero when creating invoices. If you have the necessary deductions to be added to the invoice, you can add another line item and enter a negative amount. This way, it will be deducted from the total invoice amount.
Here's a reference that you can check out:
I've also added here some resources that you can check out to help you in adding and categorising your transactions in QBSE: