Good day, Lisa Milligan,

QuickBooks Self-Employed only lets you enter the 9-digit business number. You can add the extension number on the message section of the invoice. 

Here's how:

1. Click Create invoice.
2. Enter invoice details.
3. At the lower left side of the screen, enter your business number with the extension on the Message box.
4. Send or Save as draft the invoice.

Please let me know if there's anything else I can help you with.