Yes, you can, @DarleenL.
I can share steps to ensure you can add a credit or discount amount to your bundled invoices.
First, you can manually create a service or non-inventory line item with a negative amount, and then apply it to your invoice. Here's how:
Once done, select the said item in your invoice, and then enter a negative amount if you haven't set one. Then, you'll see the said amount once you click Save and close or Save and new button on the invoice page.
If you want to know how to apply a discount to an invoice as a whole, you can refer to this article for the detailed steps: Add a discount to an invoice in QuickBooks Online.
In case you're still unable to do the said task, I suggest logging in to your account using a private window/incognito. This is to rule out the possibility of a browser-related issue due to stored cache. You can use the shortcut keys below to access one:
Then, perform the said task again. If it works this time, please clear your browser's cache to remove the piled up files that cause unusual QuickBooks Online responses. If the issue persists, you can use another supported browser instead.
Once you receive the payments from your customers, you can record them to ensure the accuracy of your records.
You can always get back to me if you have additional questions about this. I'd be happy to share a couple of solutions for you. Have a nice day.